Commit c2523fb8 authored by hjulienne's avatar hjulienne

change documentation

parent 5b4868a2
Pipeline #9947 failed with stage
in 1 minute
......@@ -4,7 +4,7 @@
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
SPHINXPROJ = Peppa-PIG
SPHINXPROJ = RAISS
SOURCEDIR = source
BUILDDIR = build
......@@ -17,4 +17,4 @@ help:
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
@ECHO OFF
pushd %~dp0
REM Command file for Sphinx documentation
if "%SPHINXBUILD%" == "" (
set SPHINXBUILD=sphinx-build
)
set SOURCEDIR=source
set BUILDDIR=build
set SPHINXPROJ=Peppa-PIG
if "%1" == "" goto help
%SPHINXBUILD% >NUL 2>NUL
if errorlevel 9009 (
echo.
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
echo.installed, then set the SPHINXBUILD environment variable to point
echo.to the full path of the 'sphinx-build' executable. Alternatively you
echo.may add the Sphinx directory to PATH.
echo.
echo.If you don't have Sphinx installed, grab it from
echo.http://sphinx-doc.org/
exit /b 1
)
%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
goto end
:help
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
:end
popd
raiss.filter\_format\_output
============================
.. automodule:: raiss.filter_format_output
.. rubric:: Functions
.. autosummary::
filter_output
\ No newline at end of file
impute\_jass.imputation\_launcher
=================================
raiss.imputation\_launcher
==========================
.. automodule:: impute_jass.imputation_launcher
.. automodule:: raiss.imputation_launcher
......
impute\_jass.ld\_matrix
=======================
raiss.ld\_matrix
================
.. automodule:: impute_jass.ld_matrix
.. automodule:: raiss.ld_matrix
......
impute\_jass.stat\_models
=========================
raiss.stat\_models
==================
.. automodule:: impute_jass.stat_models
.. automodule:: raiss.stat_models
......
impute\_jass.windows
====================
raiss.windows
=============
.. automodule:: impute_jass.windows
.. automodule:: raiss.windows
......
......@@ -14,22 +14,16 @@
#
import os
import sys
sys.path.insert(0, os.path.abspath('../..'))
#print(os.path.abspath('../..'))
sys.path.insert(0, os.path.abspath('../../raiss'))
# -- Project information -----------------------------------------------------
project = 'RAISS'
copyright = '2018, hjulienne'
author = 'hjulienne'
# The short X.Y version
version = ''
# The full version, including alpha/beta/rc tags
release = '1.0'
# -- General configuration ---------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
......@@ -110,7 +104,7 @@ html_static_path = ['_static']
# -- Options for HTMLHelp output ---------------------------------------------
# Output file base name for HTML help builder.
htmlhelp_basename = 'Peppa-PIGdoc'
htmlhelp_basename = 'RAISSdoc'
# -- Options for LaTeX output ------------------------------------------------
......@@ -137,7 +131,7 @@ latex_elements = {
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
(master_doc, 'Peppa-PIG.tex', 'Peppa-PIG Documentation',
(master_doc, 'RAISS.tex', 'RAISS Documentation',
'hjulienne', 'manual'),
]
......@@ -147,7 +141,7 @@ latex_documents = [
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
(master_doc, 'peppa-pig', 'Peppa-PIG Documentation',
(master_doc, 'raiss', 'RAISS Documentation',
[author], 1)
]
......@@ -158,8 +152,8 @@ man_pages = [
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
(master_doc, 'Peppa-PIG', 'Peppa-PIG Documentation',
author, 'Peppa-PIG', 'One line description of project.',
(master_doc, 'RAISS', 'RAISS Documentation',
author, 'RAISS', 'One line description of project.',
'Miscellaneous'),
]
......
......@@ -16,7 +16,7 @@ What is RAISS ?
RAISS is a python package to impute missing SNP summary statistics from
neighboring SNPs in linkage desiquilibrium.
The statistical model used to make the imputation is described in :cite:`Pasaniuc2014`
The statistical model used to make the imputation is described in :cite:`Pasaniuc2014` and in :cite:`lee2013dist`.
The imputation execution time is optimized by precomputing Linkage desiquilibrium between SNPs.
......@@ -101,20 +101,17 @@ Command Line Usage
.. argparse::
:ref: raiss.__main__.add_chromosome_imputation_argument
:prog: raiss
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
.. automodule:: impute_jass
.. automodule:: raiss
:members:
* :ref:`search`
.. autosummary::
:toctree: _autosummary
.. bibliography:: reference.bib
......@@ -34,3 +34,15 @@ title = {{Approximately independent linkage disequilibrium blocks in human popul
volume = {32},
year = {2015}
}
@article{lee2013dist,
title={DIST: direct imputation of summary statistics for unmeasured SNPs},
author={Lee, Donghyung and Bigdeli, T Bernard and Riley, Brien P and Fanous, Ayman H and Bacanu, Silviu-Alin},
journal={Bioinformatics},
volume={29},
number={22},
pages={2925--2927},
year={2013},
publisher={Oxford University Press}
}
"""
.. autosummary::
:toctree: _autosummary
......@@ -8,6 +7,7 @@
stat_models
windows
filter_format_output
imputation_R2
"""
import raiss.ld_matrix as LD
import raiss.stat_models as model
......
......@@ -14,7 +14,6 @@ import numpy as np
def generated_test_data(zscore, N_to_mask=5000, condition=None):
"""
Mask N_to_mask Snps in the dataframe zscore and return the dataframe with missing SNPs.
Args:
zscore (pandas DataFrame): Zscores DataFrame
condition (None or pandas boolean Series): If None, SNPs will be mask randomly. If a pandas boolean series is passed, masked SNPs will be randomly chosen inside the SNPs which have True value.
......@@ -36,7 +35,6 @@ def generated_test_data(zscore, N_to_mask=5000, condition=None):
def imputation_performance(zscore_initial, zscore_imputed, masked):
"""
two dataframe
Args:
zscore_initial (pandas DataFrame):
zscore_imputed (pandas DataFrame):
......@@ -113,8 +111,7 @@ def grid_search(zscore_folder, masked_folder, output_folder, ref_folder, ld_fold
* Masked Snps in the input dataset
for eigen ratio in **eigen_ratio_grid**:
* Impute SNPs
* Compute performance on masked SNps
* Compute performance on masked SNPs
Args:
zscore_folder (str): path toward the input data folder
masked_folder (str) : path toward the folder to save the dataframe with masked SNPs
......
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