Read the Docs build information
Build id: 509798
Project: life-epigenetics-methylcheck
Version: latest
Commit: 09d69b66ee7785d84a390b965e1838506b8b30b4
Date: 2020-12-16T21:45:58.380452Z
State: finished
Success: True


[rtd-command-info] start-time: 2020-12-16T21:46:00.268410Z, end-time: 2020-12-16T21:46:12.406737Z, duration: 12, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/FOXOBioScience/methylcheck.git .
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[rtd-command-info] start-time: 2020-12-16T21:46:12.869161Z, end-time: 2020-12-16T21:46:13.411721Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: checking out 'origin/master'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

HEAD is now at 09d69b6 Feature/mouse (#38)

[rtd-command-info] start-time: 2020-12-16T21:46:13.651937Z, end-time: 2020-12-16T21:46:13.708578Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-12-16T21:46:17.183955Z, end-time: 2020-12-16T21:46:21.503354Z, duration: 4, exit-code: 0
python3.7 -mvirtualenv --system-site-packages 
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2020-12-16T21:46:21.709044Z, end-time: 2020-12-16T21:46:23.423052Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (20.3.3)

[rtd-command-info] start-time: 2020-12-16T21:46:23.610406Z, end-time: 2020-12-16T21:46:32.701173Z, duration: 9, exit-code: 0
python -m pip install --upgrade --no-cache-dir -I setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 six commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2
Collecting commonmark==0.8.1
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Building wheels for collected packages: mock, future
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23755 sha256=26ab062113b4dae58c9a1c92e6c4cc5ecc2392781cd756031975cf02289feeb6
  Stored in directory: /tmp/pip-ephem-wheel-cache-qwjibqwk/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=e5b35b22e17681330a4a964fcde6f6bfb6084ee7f95a7d8979e164e5936942c1
  Stored in directory: /tmp/pip-ephem-wheel-cache-qwjibqwk/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
Successfully built mock future
Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible.
Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.3 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.8 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.4 readthedocs-sphinx-ext-2.1.1 recommonmark-0.5.0 requests-2.25.1 setuptools-51.0.0 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.2

[rtd-command-info] start-time: 2020-12-16T21:46:32.843126Z, end-time: 2020-12-16T21:46:44.962143Z, duration: 12, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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Collecting matplotlib<3.1.3
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Collecting jedi>=0.10
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Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (1.2.0)
Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (1.2.4)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (20.8)
Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (2.9.0)
Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (2.25.1)
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  Downloading testpath-0.4.4-py2.py3-none-any.whl (163 kB)
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Building wheels for collected packages: m2r, pandocfilters, pyrsistent
  Building wheel for m2r (setup.py): started
  Building wheel for m2r (setup.py): finished with status 'done'
  Created wheel for m2r: filename=m2r-0.2.1-py3-none-any.whl size=10465 sha256=36b82b91fe8636825e95ca7deb67c190fe03b5b9e6f8e1cefd59aeb05ee378ee
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  Building wheel for pandocfilters (setup.py): started
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  Created wheel for pandocfilters: filename=pandocfilters-1.4.3-py3-none-any.whl size=7992 sha256=8829813b39b4e07c3fde0e77e11dc3d19a1b9f212ae7e9bd2decd516596c9566
  Stored in directory: /tmp/pip-ephem-wheel-cache-tek5d7_o/wheels/42/81/34/545dc2fbf0e9137811e901108d37fc04650e81d48f97078000
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  Created wheel for pyrsistent: filename=pyrsistent-0.17.3-cp37-cp37m-linux_x86_64.whl size=115338 sha256=3e49a04419c178491fe5b671df79b7b07340525bd1c7269b8fba654eeaa96fab
  Stored in directory: /tmp/pip-ephem-wheel-cache-tek5d7_o/wheels/a5/52/bf/71258a1d7b3c8cbe1ee53f9314c6f65f20385481eaee573cc5
Successfully built m2r pandocfilters pyrsistent
Installing collected packages: zipp, typing-extensions, ipython-genutils, traitlets, pyrsistent, importlib-metadata, attrs, tornado, pyzmq, jupyter-core, jsonschema, webencodings, wcwidth, ptyprocess, parso, nest-asyncio, nbformat, jupyter-client, async-generator, testpath, prompt-toolkit, pickleshare, pexpect, pandocfilters, nbclient, mistune, jupyterlab-pygments, jedi, entrypoints, defusedxml, decorator, bleach, backcall, pbr, nbconvert, matplotlib, ipython, xlrd, tqdm, sphinxcontrib-apidoc, seaborn, nbsphinx, m2r, joblib, ipykernel
  Attempting uninstall: matplotlib
    Found existing installation: matplotlib 3.3.2
    Not uninstalling matplotlib at /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest
    Can't uninstall 'matplotlib'. No files were found to uninstall.
Successfully installed async-generator-1.10 attrs-20.3.0 backcall-0.2.0 bleach-3.2.1 decorator-4.4.2 defusedxml-0.6.0 entrypoints-0.3 importlib-metadata-3.3.0 ipykernel-5.4.2 ipython-7.19.0 ipython-genutils-0.2.0 jedi-0.17.2 joblib-1.0.0 jsonschema-3.2.0 jupyter-client-6.1.7 jupyter-core-4.7.0 jupyterlab-pygments-0.1.2 m2r-0.2.1 matplotlib-3.1.2 mistune-0.8.4 nbclient-0.5.1 nbconvert-6.0.7 nbformat-5.0.8 nbsphinx-0.8.0 nest-asyncio-1.4.3 pandocfilters-1.4.3 parso-0.7.1 pbr-5.5.1 pexpect-4.8.0 pickleshare-0.7.5 prompt-toolkit-3.0.8 ptyprocess-0.6.0 pyrsistent-0.17.3 pyzmq-20.0.0 seaborn-0.11.0 sphinxcontrib-apidoc-0.3.0 testpath-0.4.4 tornado-6.1 tqdm-4.54.1 traitlets-5.0.5 typing-extensions-3.7.4.3 wcwidth-0.2.5 webencodings-0.5.1 xlrd-2.0.1 zipp-3.4.0

[rtd-command-info] start-time: 2020-12-16T21:46:46.772454Z, end-time: 2020-12-16T21:46:46.844964Z, duration: 0, exit-code: 0
cat conf.py
# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config

# -- Path setup --------------------------------------------------------------

# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
import os
import sys
sys.path.insert(0, os.path.abspath('.'))


# -- Project information -----------------------------------------------------

project = 'methylcheck'
copyright = '2020, FOXO Bioscience'
author = 'FOXO Bioscience'

# The short X.Y version
version = '0.7'
# The full version, including alpha/beta/rc tags
release = '0.7'


# -- General configuration ---------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    'sphinx.ext.autodoc',
    'sphinxcontrib.apidoc',
    'm2r',
    'nbsphinx',
    'sphinx.ext.autosummary'
]

# instead of CLI "sphinx-autodoc . _build/html" you write this
apidoc_module_dir = '.'
apidoc_output_dir = '_sphinx_build'
apidoc_excluded_paths = ['tests']
apidoc_separate_modules = False

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_sphinx_templates']

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
source_suffix = ['.rst', '.md']
# source_suffix = '.rst'

# The master toctree document.
master_doc = 'index'

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path .
exclude_patterns = ['_sphinx_build', 'Thumbs.db', '.DS_Store']

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'


# -- Options for HTML output -------------------------------------------------

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
#
html_theme =  'sphinx_rtd_theme' #'alabaster'

# Theme options are theme-specific and customize the look and feel of a theme
# further.  For a list of options available for each theme, see the
# documentation.
#
# html_theme_options = {}

# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_sphinx_static']

# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# The default sidebars (for documents that don't match any pattern) are
# defined by theme itself.  Builtin themes are using these templates by
# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
# 'searchbox.html']``.
#
# html_sidebars = {}


# -- Options for HTMLHelp output ---------------------------------------------

# Output file base name for HTML help builder.
htmlhelp_basename = 'methylcheckdoc'


# -- Options for LaTeX output ------------------------------------------------

latex_elements = {
    # The paper size ('letterpaper' or 'a4paper').
    #
    # 'papersize': 'letterpaper',

    # The font size ('10pt', '11pt' or '12pt').
    #
    # 'pointsize': '10pt',

    # Additional stuff for the LaTeX preamble.
    #
    # 'preamble': '',

    # Latex figure (float) alignment
    #
    # 'figure_align': 'htbp',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
#  author, documentclass [howto, manual, or own class]).
latex_documents = [
    (master_doc, 'methylcheck.tex', 'methylcheck Documentation',
     'Life Epigenetics', 'manual'),
]


# -- Options for manual page output ------------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    (master_doc, 'methylcheck', 'methylcheck Documentation',
     [author], 1)
]


# -- Options for Texinfo output ----------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
#  dir menu entry, description, category)
texinfo_documents = [
    (master_doc, 'methylcheck', 'methylcheck Documentation',
     author, 'methylcheck', 'One line description of project.',
     'Miscellaneous'),
]


# -- Extension configuration -------------------------------------------------




###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#


import importlib
import sys
import os.path
from six import string_types

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    elif isinstance(source_suffix, (list, tuple)):
        # Sphinx >= 1.3 supports list/tuple to define multiple suffixes
        SUFFIX = source_suffix[0]
    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
    html_static_path = []
if os.path.exists('_static'):
    html_static_path.append('_static')

# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = (
    (
        'html_theme' in globals() and
        html_theme in ['default'] and
        # Allow people to bail with a hack of having an html_style
        'html_style' not in globals()
    ) or 'html_theme' not in globals()
)
if using_rtd_theme:
    theme = importlib.import_module('sphinx_rtd_theme')
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'https://readthedocs.com/websupport'
    websupport2_static_url = 'https://assets.readthedocs.com/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "latest",
    'version_slug': "latest",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ("feature-mouse", "/en/feature-mouse/"),
    ],
    'downloads': [ 
    ("pdf", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/latest/pdf/"),
    ("html", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"),
    ("epub", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/latest/epub/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'life-epigenetics-methylcheck',
    'name': u'methylcheck',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://life-epigenetics-methylcheck.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'FOXOBioScience',
    'proxied_api_host': '/_',
    'github_repo': 'methylcheck',
    'github_version': 'master',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'master',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'master',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '09d69b66',
}




if 'html_context' in globals():
    
    html_context.update(context)
    
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2020-12-16T21:46:47.151606Z, end-time: 2020-12-16T21:47:52.302531Z, duration: 65, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/conf.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/setup.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.data_files.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.predict.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.probes.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.samples.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/modules.rst.
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 24 source files that are out of date
updating environment: 24 added, 0 changed, 0 removed
reading sources... [  4%] README
reading sources... [  8%] docs/example_notebooks/another-methylcheck-qc-example
reading sources... [ 12%] docs/example_notebooks/demo-methylprep-to-methylcheck-example
reading sources... [ 16%] docs/example_notebooks/demo_read_geo_processed
reading sources... [ 20%] docs/example_notebooks/demo_using_matched_meta_data
reading sources... [ 25%] docs/example_notebooks/examples
reading sources... [ 29%] docs/example_notebooks/interactive-mds-filtering
reading sources... [ 33%] docs/example_notebooks/methylcheck-cli
reading sources... [ 37%] docs/example_notebooks/methylprep-methylcheck-qc-example
reading sources... [ 41%] docs/example_notebooks/outdated-methylprep-methylcheck-example
reading sources... [ 45%] docs/example_notebooks/postprocessQC_example
reading sources... [ 50%] docs/example_notebooks/pval
reading sources... [ 54%] docs/example_notebooks/qc-sex-check
reading sources... [ 58%] docs/example_notebooks/rawQC_example
reading sources... [ 62%] docs/example_notebooks/testing_sns_upgrade_methylcheck_v0.6.2
reading sources... [ 66%] docs/filtering-probes
reading sources... [ 70%] docs/loading-data
reading sources... [ 75%] docs/quality-control-example
reading sources... [ 79%] docs/release-history
reading sources... [ 83%] docs/research_notebooks/postprocessQC_example
reading sources... [ 87%] docs/research_notebooks/pval
reading sources... [ 91%] docs/research_notebooks/rawQC_example
reading sources... [ 95%] docs/source/modules
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md:: WARNING: image file not readable: docs/example_notebooks/tutorial_figs/fig1.png
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md:: WARNING: image file not readable: docs/example_notebooks/tutorial_figs/fig2.png
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md:: WARNING: image file not readable: docs/example_notebooks/tutorial_figs/fig3.png
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md:: WARNING: image file not readable: docs/example_notebooks/tutorial_figs/fig4.png
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md:: WARNING: image file not readable: docs/example_notebooks/tutorial_figs/fig5.png
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md:: WARNING: image file not readable: docs/example_notebooks/tutorial_figs/fig6.png
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md:: WARNING: image file not readable: docs/example_notebooks/tutorial_figs/fig7.png
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylprep-methylcheck-qc-example.ipynb:295: WARNING: Title level inconsistent:

next, remove all probes that researchers have deemed inreliable
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylprep-methylcheck-qc-example.ipynb:404: WARNING: Title level inconsistent:

MDS filtering
~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/outdated-methylprep-methylcheck-example.ipynb:295: WARNING: Title level inconsistent:

next, remove all probes that researchers have deemed inreliable
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/outdated-methylprep-methylcheck-example.ipynb:404: WARNING: Title level inconsistent:

MDS filtering
~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/postprocessQC_example.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/rawQC_example.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/testing_sns_upgrade_methylcheck_v0.6.2.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering-probes.ipynb:399: WARNING: Title level inconsistent:

Be careful -- you can apply the a probe list for EPIC to a 450k dataset, and it will work, but won't be good filtering.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering-probes.ipynb:451: WARNING: Title level inconsistent:

Maximum filtering happens by default.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering-probes.ipynb:524: WARNING: Title level inconsistent:

Take a look at other quality control methods, such as MDS and cumulative\_sum found in other example notebooks.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/loading-data.ipynb:683: WARNING: Title level inconsistent:

'meth\_df' format
~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/loading-data.ipynb:758: WARNING: Title level inconsistent:

'noob\_df' format
~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/loading-data.ipynb:833: WARNING: Title level inconsistent:

'meth' format will return a list of Python SampleDataContainer objects.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/loading-data.ipynb:912: WARNING: Title level inconsistent:

Loading CSVs using Pandas
~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/loading-data.ipynb:1211: WARNING: Title level inconsistent:

'm\_value'
~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/postprocessQC_example.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cli'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_pipeline'
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.get_sex'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.assign'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:85: WARNING: Unknown directive type "todo".

.. todo::
    - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs
    - DONE: meth_df deal with batches of files
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:4: WARNING: Unexpected section title.

options:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:17: WARNING: Unexpected section title.

example:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:24: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:27: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_report.py:docstring of methylcheck.qc_report.run_pipeline:25: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:4: WARNING: Unexpected section title.

Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:7: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:10: WARNING: Unexpected section title.

Optional Arguments
------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:25: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:8: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:13: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:18: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:26: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:16: WARNING: Unexpected section title or transition.

----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:18: WARNING: Unexpected section title.

Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:24: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:52: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:49: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:66: WARNING: Unexpected section title or transition.

-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:68: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.sample_plot:1: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:4: WARNING: Unexpected section title.

Arguments
---------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:31: WARNING: Unexpected section title.

Options
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:42: WARNING: Unexpected section title.

returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:47: WARNING: Unexpected section title.

requires
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:52: WARNING: Unexpected section title.

notes
-----
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:56: WARNING: Unknown directive type "todo".

.. todo::

    - Reads the manifest file for the array, or at least a list of probe names to exclude/include.
    - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']]
    - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values
    - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values
    df_no_sex_probes = df[probe_names_no_sex_probes]
    df_no_sex_probes.head()
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_compare:3: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:3: WARNING: Unexpected section title or transition.

--------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:5: WARNING: Unexpected section title.

how it works:
--------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:18: WARNING: Unexpected section title or transition.

-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:20: WARNING: Unexpected section title.

inputs:
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:28: WARNING: Unexpected section title.

optional keyword arguments:
---------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:40: WARNING: Unexpected section title.

analysis parameters:
--------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:47: WARNING: Unexpected section title.

returns:
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:51: WARNING: Unknown directive type "todo".

.. todo::
    - TODO: one dataframe of the retained samples, cutoff box is avg of datasets
    - TODO: each dataset's results as a transformed file
    - default: list of samples retained or excluded
    - option: a list of pyplot subplot objects
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:4: WARNING: Unexpected section title.

input (one of these):
=====================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:23: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:26: WARNING: Unexpected section title.

optional params:
================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:4: WARNING: Unexpected section title.

input (choose one of these):
============================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:34: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:5: WARNING: Unexpected section title.

input:
======
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:11: WARNING: Unexpected section title.

options:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:14: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/predict/__init__.py:docstring of methylcheck.predict.get_sex:4: WARNING: Unexpected section title.

inputs:
=======
WARNING: autodoc: failed to import module 'p_value_probe_detection' from module 'methylcheck'; the following exception was raised:
No module named 'statsmodels'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_report.py:docstring of methylcheck.qc_report.ReportPDF:43: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_report.py:docstring of methylcheck.qc_report.ReportPDF:41: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_report.py:docstring of methylcheck.qc_report.ReportPDF:41: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_report.py:docstring of methylcheck.qc_report.ReportPDF:51: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:44: WARNING: Unknown target name: "gse150999".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load_both:15: WARNING: Unknown target name: "gse150999".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:19: WARNING: Unknown target name: "matrix".
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/another-methylcheck-qc-example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo-methylprep-to-methylcheck-example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo_read_geo_processed.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo_using_matched_meta_data.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/interactive-mds-filtering.ipynb: WARNING: document isn't included in any toctree
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/outdated-methylprep-methylcheck-example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/pval.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/qc-sex-check.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/testing_sns_upgrade_methylcheck_v0.6.2.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/pval.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [  4%] README
writing output... [  8%] docs/example_notebooks/another-methylcheck-qc-example
writing output... [ 12%] docs/example_notebooks/demo-methylprep-to-methylcheck-example
writing output... [ 16%] docs/example_notebooks/demo_read_geo_processed
writing output... [ 20%] docs/example_notebooks/demo_using_matched_meta_data
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[rtd-command-info] start-time: 2020-12-16T21:47:52.647500Z, end-time: 2020-12-16T21:48:02.802492Z, duration: 10, exit-code: 0
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next, remove all probes that researchers have deemed inreliable
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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MDS filtering
~~~~~~~~~~~~~
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next, remove all probes that researchers have deemed inreliable
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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MDS filtering
~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/postprocessQC_example.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/rawQC_example.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/testing_sns_upgrade_methylcheck_v0.6.2.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering-probes.ipynb:399: WARNING: Title level inconsistent:

Be careful -- you can apply the a probe list for EPIC to a 450k dataset, and it will work, but won't be good filtering.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Maximum filtering happens by default.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Take a look at other quality control methods, such as MDS and cumulative\_sum found in other example notebooks.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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'meth\_df' format
~~~~~~~~~~~~~~~~~
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'noob\_df' format
~~~~~~~~~~~~~~~~~
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'meth' format will return a list of Python SampleDataContainer objects.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Loading CSVs using Pandas
~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/loading-data.ipynb:1211: WARNING: Title level inconsistent:

'm\_value'
~~~~~~~~~~
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_M_vs_U'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_controls'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_beta_by_type'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.list_problem_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.drop_nan_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.samples'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.sample_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_density_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_compare'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_mds_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.combine_mds'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.predict'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.get_sex'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.assign'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:85: WARNING: Unknown directive type "todo".

.. todo::
    - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs
    - DONE: meth_df deal with batches of files
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:4: WARNING: Unexpected section title.

options:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:17: WARNING: Unexpected section title.

example:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:24: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:27: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_report.py:docstring of methylcheck.qc_report.run_pipeline:25: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:4: WARNING: Unexpected section title.

Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:7: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:10: WARNING: Unexpected section title.

Optional Arguments
------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:25: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:8: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:13: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:18: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:26: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:16: WARNING: Unexpected section title or transition.

----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:18: WARNING: Unexpected section title.

Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:24: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:52: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:49: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:66: WARNING: Unexpected section title or transition.

-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:68: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.sample_plot:1: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:4: WARNING: Unexpected section title.

Arguments
---------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:31: WARNING: Unexpected section title.

Options
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:42: WARNING: Unexpected section title.

returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:47: WARNING: Unexpected section title.

requires
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:52: WARNING: Unexpected section title.

notes
-----
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:56: WARNING: Unknown directive type "todo".

.. todo::

    - Reads the manifest file for the array, or at least a list of probe names to exclude/include.
    - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']]
    - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values
    - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values
    df_no_sex_probes = df[probe_names_no_sex_probes]
    df_no_sex_probes.head()
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_compare:3: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:3: WARNING: Unexpected section title or transition.

--------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:5: WARNING: Unexpected section title.

how it works:
--------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:18: WARNING: Unexpected section title or transition.

-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:20: WARNING: Unexpected section title.

inputs:
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:28: WARNING: Unexpected section title.

optional keyword arguments:
---------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:40: WARNING: Unexpected section title.

analysis parameters:
--------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:47: WARNING: Unexpected section title.

returns:
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:51: WARNING: Unknown directive type "todo".

.. todo::
    - TODO: one dataframe of the retained samples, cutoff box is avg of datasets
    - TODO: each dataset's results as a transformed file
    - default: list of samples retained or excluded
    - option: a list of pyplot subplot objects
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:4: WARNING: Unexpected section title.

input (one of these):
=====================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:23: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:26: WARNING: Unexpected section title.

optional params:
================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:4: WARNING: Unexpected section title.

input (choose one of these):
============================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:34: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:5: WARNING: Unexpected section title.

input:
======
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:11: WARNING: Unexpected section title.

options:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:14: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/predict/__init__.py:docstring of methylcheck.predict.get_sex:4: WARNING: Unexpected section title.

inputs:
=======
WARNING: autodoc: failed to import module 'p_value_probe_detection' from module 'methylcheck'; the following exception was raised:
No module named 'statsmodels'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_report.py:docstring of methylcheck.qc_report.ReportPDF:43: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_report.py:docstring of methylcheck.qc_report.ReportPDF:41: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_report.py:docstring of methylcheck.qc_report.ReportPDF:41: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_report.py:docstring of methylcheck.qc_report.ReportPDF:51: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:44: WARNING: Unknown target name: "gse150999".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load_both:15: WARNING: Unknown target name: "gse150999".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:19: WARNING: Unknown target name: "matrix".
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/another-methylcheck-qc-example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo-methylprep-to-methylcheck-example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo_read_geo_processed.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo_using_matched_meta_data.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/interactive-mds-filtering.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylprep-methylcheck-qc-example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/outdated-methylprep-methylcheck-example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/pval.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/qc-sex-check.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/testing_sns_upgrade_methylcheck_v0.6.2.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/pval.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done
assembling single document... docs/loading-data docs/quality-control-example docs/filtering-probes docs/example_notebooks/examples docs/source/modules docs/source/_autosummary/methylcheck.cli /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.cli'
docs/source/_autosummary/methylcheck.run_pipeline /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.run_pipeline'
docs/source/_autosummary/methylcheck.run_qc /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.run_qc'
docs/source/_autosummary/methylcheck.read_geo /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.read_geo'
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next, remove all probes that researchers have deemed inreliable
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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MDS filtering
~~~~~~~~~~~~~
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next, remove all probes that researchers have deemed inreliable
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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MDS filtering
~~~~~~~~~~~~~
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Be careful -- you can apply the a probe list for EPIC to a 450k dataset, and it will work, but won't be good filtering.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Maximum filtering happens by default.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Take a look at other quality control methods, such as MDS and cumulative\_sum found in other example notebooks.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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'meth\_df' format
~~~~~~~~~~~~~~~~~
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'noob\_df' format
~~~~~~~~~~~~~~~~~
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'meth' format will return a list of Python SampleDataContainer objects.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Loading CSVs using Pandas
~~~~~~~~~~~~~~~~~~~~~~~~~
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'm\_value'
~~~~~~~~~~
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.list_problem_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.drop_nan_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.samples'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.sample_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_density_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_compare'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_mds_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.combine_mds'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.predict'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.get_sex'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.assign'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:85: WARNING: Unknown directive type "todo".

.. todo::
    - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs
    - DONE: meth_df deal with batches of files
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:4: WARNING: Unexpected section title.

options:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:17: WARNING: Unexpected section title.

example:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:24: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:27: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_report.py:docstring of methylcheck.qc_report.run_pipeline:25: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:4: WARNING: Unexpected section title.

Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:7: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:10: WARNING: Unexpected section title.

Optional Arguments
------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:25: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:8: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:13: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:18: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:26: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:16: WARNING: Unexpected section title or transition.

----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:18: WARNING: Unexpected section title.

Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:24: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:52: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:49: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:66: WARNING: Unexpected section title or transition.

-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:68: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.sample_plot:1: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:4: WARNING: Unexpected section title.

Arguments
---------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:31: WARNING: Unexpected section title.

Options
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:42: WARNING: Unexpected section title.

returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:47: WARNING: Unexpected section title.

requires
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:52: WARNING: Unexpected section title.

notes
-----
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:56: WARNING: Unknown directive type "todo".

.. todo::

    - Reads the manifest file for the array, or at least a list of probe names to exclude/include.
    - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']]
    - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values
    - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values
    df_no_sex_probes = df[probe_names_no_sex_probes]
    df_no_sex_probes.head()
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_compare:3: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:3: WARNING: Unexpected section title or transition.

--------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:5: WARNING: Unexpected section title.

how it works:
--------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:18: WARNING: Unexpected section title or transition.

-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:20: WARNING: Unexpected section title.

inputs:
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:28: WARNING: Unexpected section title.

optional keyword arguments:
---------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:40: WARNING: Unexpected section title.

analysis parameters:
--------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:47: WARNING: Unexpected section title.

returns:
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:51: WARNING: Unknown directive type "todo".

.. todo::
    - TODO: one dataframe of the retained samples, cutoff box is avg of datasets
    - TODO: each dataset's results as a transformed file
    - default: list of samples retained or excluded
    - option: a list of pyplot subplot objects
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:4: WARNING: Unexpected section title.

input (one of these):
=====================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:23: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:26: WARNING: Unexpected section title.

optional params:
================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:4: WARNING: Unexpected section title.

input (choose one of these):
============================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:34: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:5: WARNING: Unexpected section title.

input:
======
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:11: WARNING: Unexpected section title.

options:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:14: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/predict/__init__.py:docstring of methylcheck.predict.get_sex:4: WARNING: Unexpected section title.

inputs:
=======
WARNING: autodoc: failed to import module 'p_value_probe_detection' from module 'methylcheck'; the following exception was raised:
No module named 'statsmodels'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_report.py:docstring of methylcheck.qc_report.ReportPDF:43: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_report.py:docstring of methylcheck.qc_report.ReportPDF:41: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_report.py:docstring of methylcheck.qc_report.ReportPDF:41: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_report.py:docstring of methylcheck.qc_report.ReportPDF:51: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:44: WARNING: Unknown target name: "gse150999".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load_both:15: WARNING: Unknown target name: "gse150999".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:19: WARNING: Unknown target name: "matrix".
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/another-methylcheck-qc-example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo-methylprep-to-methylcheck-example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo_read_geo_processed.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/demo_using_matched_meta_data.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/interactive-mds-filtering.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylprep-methylcheck-qc-example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/outdated-methylprep-methylcheck-example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/pval.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/qc-sex-check.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/testing_sns_upgrade_methylcheck_v0.6.2.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/pval.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree
done
processing methylcheck.tex...index docs/loading-data docs/quality-control-example docs/filtering-probes docs/example_notebooks/examples docs/source/modules docs/source/_autosummary/methylcheck.cli /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.cli'
docs/source/_autosummary/methylcheck.run_pipeline /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.run_pipeline'
docs/source/_autosummary/methylcheck.run_qc /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.run_qc'
docs/source/_autosummary/methylcheck.read_geo docs/source/_autosummary/methylcheck.load /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.read_geo'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.load'
docs/source/_autosummary/methylcheck.load_both /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.load_both'
docs/source/_autosummary/methylcheck.qc_signal_intensity /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.qc_signal_intensity'
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cat latexmkrc
$latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S';
$makeindex = 'makeindex -s python.ist %O -o %D %S';
add_cus_dep( "glo", "gls", 0, "makeglo" );
sub makeglo {
 return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
}

[rtd-command-info] start-time: 2020-12-16T21:48:19.733680Z, end-time: 2020-12-16T21:48:30.882684Z, duration: 11, exit-code: 0
latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=life-epigenetics-methylcheck -interaction=nonstopmode
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                                                  ^^M

! LaTeX Error: Unknown graphics extension: .svg.

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l.236 ...3/aedf5c223e39415180ff35153b2bad89}.svg}}
                                                  ^^M

! LaTeX Error: Unknown graphics extension: .svg.

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l.236 ...3/aedf5c223e39415180ff35153b2bad89}.svg}}
                                                  ^^M

! LaTeX Error: Unknown graphics extension: .svg.

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l.238 ...a5887c2be8734c7efa000abd8618/badge}.svg}}
                                                  ^^M

! LaTeX Error: Unknown graphics extension: .svg.

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l.238 ...a5887c2be8734c7efa000abd8618/badge}.svg}}
                                                  ^^M

LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epi
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LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epi
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Overfull \hbox (975.67087pt too wide) in paragraph at lines 2--243
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[1] [2 <./methylcheck_overview.png>]
Chapter 1.
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[3] [4 <./methylcheck_functions.png>]
Chapter 2.
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Chapter 3.
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Chapter 4.
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Chapter 5.
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Chapter 6.
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[16]

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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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[18]

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Type  H <return>  for immediate help.
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Overfull \vbox (1.32576pt too high) detected at line 872
[19]

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(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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! Package inputenc Error: Unicode char █ (U+2588)
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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Type  H <return>  for immediate help.
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Underfull \vbox (badness 3492) detected at line 1135
[22]
Underfull \vbox (badness 10000) detected at line 1146
[23 <./docs_quality-control-example_5_0.png>]
Underfull \vbox (badness 10000) detected at line 1157
[24 <./docs_quality-control-example_5_1.png>]
Underfull \vbox (badness 10000) detected at line 1168
[25 <./docs_quality-control-example_5_2.png>]
Underfull \vbox (badness 10000) detected at line 1179
[26 <./docs_quality-control-example_5_3.png>]
Underfull \vbox (badness 10000) detected at line 1190
[27 <./docs_quality-control-example_5_4.png>]
Underfull \vbox (badness 10000) detected at line 1201
[28 <./docs_quality-control-example_5_5.png>]
Underfull \vbox (badness 10000) detected at line 1212
[29 <./docs_quality-control-example_5_6.png>]
Underfull \vbox (badness 10000) detected at line 1223
[30 <./docs_quality-control-example_5_7.png>]
Underfull \vbox (badness 10000) detected at line 1234
[31 <./docs_quality-control-example_5_8.png>]
Underfull \vbox (badness 10000) detected at line 1272
[32 <./docs_quality-control-example_5_9.png>]
Underfull \vbox (badness 10000) detected at line 1309
[33 <./docs_quality-control-example_5_12.png>]
Underfull \vbox (badness 10000) detected at line 1346
[34 <./docs_quality-control-example_5_15.png>]
Underfull \vbox (badness 10000) detected at line 1383
[35 <./docs_quality-control-example_5_18.png>]
Underfull \vbox (badness 10000) detected at line 1404
[36 <./docs_quality-control-example_5_21.png>]
Underfull \vbox (badness 10000) detected at line 1415
[37 <./docs_quality-control-example_6_0.png>]
Underfull \vbox (badness 10000) detected at line 1426
[38 <./docs_quality-control-example_6_1.png>]
Underfull \vbox (badness 10000) detected at line 1437
[39 <./docs_quality-control-example_6_2.png>]
Underfull \vbox (badness 10000) detected at line 1448
[40 <./docs_quality-control-example_6_3.png>]
Underfull \vbox (badness 10000) detected at line 1459
[41 <./docs_quality-control-example_6_4.png>]
Underfull \vbox (badness 10000) detected at line 1470
[42 <./docs_quality-control-example_6_5.png>]
Underfull \vbox (badness 10000) detected at line 1481
[43 <./docs_quality-control-example_6_6.png>]
Underfull \vbox (badness 10000) detected at line 1492
[44 <./docs_quality-control-example_6_7.png>]
Underfull \vbox (badness 10000) detected at line 1503
[45 <./docs_quality-control-example_6_8.png>]
Underfull \vbox (badness 10000) detected at line 1540
[46 <./docs_quality-control-example_6_9.png>]
Underfull \vbox (badness 10000) detected at line 1564
[47 <./docs_quality-control-example_6_12.png>]
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[48 <./docs_quality-control-example_6_14.png>]
Underfull \vbox (badness 10000) detected at line 1612
[49 <./docs_quality-control-example_6_16.png>] [50 <./docs_quality-control-exam
ple_6_18.png>] [51] [52]

! Package inputenc Error: Unicode char █ (U+2588)
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See the inputenc package documentation for explanation.
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! Package inputenc Error: Unicode char █ (U+2588)
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See the inputenc package documentation for explanation.
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! Package inputenc Error: Unicode char █ (U+2588)
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See the inputenc package documentation for explanation.
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! Package inputenc Error: Unicode char █ (U+2588)
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See the inputenc package documentation for explanation.
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! Package inputenc Error: Unicode char █ (U+2588)
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See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
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See the inputenc package documentation for explanation.
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! Package inputenc Error: Unicode char █ (U+2588)
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See the inputenc package documentation for explanation.
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! Package inputenc Error: Unicode char █ (U+2588)
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See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
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See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
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See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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[71] [72] [73] [74]
Chapter 7.
[75] [76]

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Chapter 1.

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Chapter 2.
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Chapter 3.
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Chapter 4.
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Chapter 5.
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See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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Overfull \vbox (1.63934pt too high) detected at line 650
[17]

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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[18]

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.763 ...��███| 6/6 [00:01<00:00,  3.68it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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Overfull \vbox (1.32576pt too high) detected at line 872
[19]

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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[20]

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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[21]

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
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lue'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file_stem=''\T1/ptm/m/n/10 ,

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[]\T1/ptm/m/n/10 this is for load-ing a bunch of pro-cessed csv files into con-
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\T1/ptm/m/n/10 tas \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 import methylcheck as m fil
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\T1/pcr/m/n/10 containers = m.load(files, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 meth\
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ce2013\TS1/pcr/m/n/10 '
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[]\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Polymorphism\TS1/pcr/m/n/10 ' '\T1/pcr/m/n/10
 CrossHybridization\TS1/pcr/m/n/10 '

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[]\T1/ptm/m/n/10 if you chose \T1/ptm/m/it/10 pro-cess ^^Uall \T1/ptm/m/n/10 yo
u can load the raw in-ten-si-ties like

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\T1/ptm/m/n/10 this, and pass them in: meth = pd.read_pickle(`meth_values.pkl')
 un-meth =
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Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.475 ...��███| 1/1 [00:00<00:00, 50.68it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.475 ...��███| 1/1 [00:00<00:00, 50.68it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.475 ...��███| 1/1 [00:00<00:00, 50.68it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.475 ...��███| 1/1 [00:00<00:00, 50.68it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.475 ...��███| 1/1 [00:00<00:00, 50.68it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.479 ...��███| 1/1 [00:00<00:00,  9.42it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.479 ...��███| 1/1 [00:00<00:00,  9.42it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.479 ...��███| 1/1 [00:00<00:00,  9.42it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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l.479 ...��███| 1/1 [00:00<00:00,  9.42it/s]
                                                  

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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[16]

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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Overfull \vbox (1.63934pt too high) detected at line 650
[17]

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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[18]

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
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! Package inputenc Error: Unicode char █ (U+2588)
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ple_6_18.png>] [51] [52]

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[79] [80]) (./life-epigenetics-methylcheck.aux) )
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Transcript written on life-epigenetics-methylcheck.log.
Latexmk: Index file 'life-epigenetics-methylcheck.idx' was written
Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/d8957073936d10691e0c27e66001ab7bf2cbab61/python3.6}.pngheight=50">`' from line
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Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/d8957073936d10691e0c27e66001ab7bf2cbab61/python3.6}.pngheight=50">`' from line
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Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/d8957073936d10691e0c27e66001ab7bf2cbab61/python3.6}.pngheight=50">`' from line
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Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/d8957073936d10691e0c27e66001ab7bf2cbab61/python3.6}.pngheight=50">`' from line
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Latexmk: Log file says output to 'life-epigenetics-methylcheck.pdf'
Collected error summary (may duplicate other messages):
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Latexmk: Errors, in force_mode: so I tried finishing targets

[rtd-command-info] start-time: 2020-12-16T21:48:31.154093Z, end-time: 2020-12-16T21:48:31.207958Z, duration: 0, exit-code: 0
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md:: WARNING: image file not readable: docs/example_notebooks/tutorial_figs/fig6.png
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylcheck-cli.md:: WARNING: image file not readable: docs/example_notebooks/tutorial_figs/fig7.png
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylprep-methylcheck-qc-example.ipynb:295: WARNING: Title level inconsistent:

next, remove all probes that researchers have deemed inreliable
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/methylprep-methylcheck-qc-example.ipynb:404: WARNING: Title level inconsistent:

MDS filtering
~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/outdated-methylprep-methylcheck-example.ipynb:295: WARNING: Title level inconsistent:

next, remove all probes that researchers have deemed inreliable
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/outdated-methylprep-methylcheck-example.ipynb:404: WARNING: Title level inconsistent:

MDS filtering
~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/postprocessQC_example.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/rawQC_example.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/example_notebooks/testing_sns_upgrade_methylcheck_v0.6.2.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering-probes.ipynb:399: WARNING: Title level inconsistent:

Be careful -- you can apply the a probe list for EPIC to a 450k dataset, and it will work, but won't be good filtering.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering-probes.ipynb:451: WARNING: Title level inconsistent:

Maximum filtering happens by default.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering-probes.ipynb:524: WARNING: Title level inconsistent:

Take a look at other quality control methods, such as MDS and cumulative\_sum found in other example notebooks.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/loading-data.ipynb:683: WARNING: Title level inconsistent:

'meth\_df' format
~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/loading-data.ipynb:758: WARNING: Title level inconsistent:

'noob\_df' format
~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/loading-data.ipynb:833: WARNING: Title level inconsistent:

'meth' format will return a list of Python SampleDataContainer objects.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/loading-data.ipynb:912: WARNING: Title level inconsistent:

Loading CSVs using Pandas
~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/loading-data.ipynb:1211: WARNING: Title level inconsistent:

'm\_value'
~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/postprocessQC_example.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb:6: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cli'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_pipeline'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_qc'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.read_geo'
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_controls'
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.predict'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.get_sex'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.assign'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:85: WARNING: Unknown directive type "todo".

.. todo::
    - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs
    - DONE: meth_df deal with batches of files
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:4: WARNING: Unexpected section title.

options:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:17: WARNING: Unexpected section title.

example:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:24: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:27: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_report.py:docstring of methylcheck.qc_report.run_pipeline:25: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:4: WARNING: Unexpected section title.

Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:7: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:10: WARNING: Unexpected section title.

Optional Arguments
------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:25: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:8: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:13: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:18: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:26: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:16: WARNING: Unexpected section title or transition.

----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:18: WARNING: Unexpected section title.

Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:24: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:52: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:49: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:66: WARNING: Unexpected section title or transition.

-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:68: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.sample_plot:1: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:4: WARNING: Unexpected section title.

Arguments
---------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:31: WARNING: Unexpected section title.

Options
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:42: WARNING: Unexpected section title.

returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:47: WARNING: Unexpected section title.

requires
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:52: WARNING: Unexpected section title.

notes
-----
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:56: WARNING: Unknown directive type "todo".

.. todo::

    - Reads the manifest file for the array, or at least a list of probe names to exclude/include.
    - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']]
    - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values
    - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values
    df_no_sex_probes = df[probe_names_no_sex_probes]
    df_no_sex_probes.head()
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_compare:3: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:3: WARNING: Unexpected section title or transition.

--------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:5: WARNING: Unexpected section title.

how it works:
--------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:18: WARNING: Unexpected section title or transition.

-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:20: WARNING: Unexpected section title.

inputs:
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:28: WARNING: Unexpected section title.

optional keyword arguments:
---------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:40: WARNING: Unexpected section title.

analysis parameters:
--------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:47: WARNING: Unexpected section title.

returns:
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:51: WARNING: Unknown directive type "todo".

.. todo::
    - TODO: one dataframe of the retained samples, cutoff box is avg of datasets
    - TODO: each dataset's results as a transformed file
    - default: list of samples retained or excluded
    - option: a list of pyplot subplot objects
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:4: WARNING: Unexpected section title.

input (one of these):
=====================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:23: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:26: WARNING: Unexpected section title.

optional params:
================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:4: WARNING: Unexpected section title.

input (choose one of these):
============================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:34: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:5: WARNING: Unexpected section title.

input:
======
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:11: WARNING: Unexpected section title.

options:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:14: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/predict/__init__.py:docstring of methylcheck.predict.get_sex:4: WARNING: Unexpected section title.

inputs:
=======
WARNING: autodoc: failed to import module 'p_value_probe_detection' from module 'methylcheck'; the following exception was raised:
No module named 'statsmodels'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_report.py:docstring of methylcheck.qc_report.ReportPDF:43: WARNING: Unexpected indentation.
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