Commit f9b63857 authored by Hanna  JULIENNE's avatar Hanna JULIENNE

added some documentation

parent 9c7fffed
......@@ -45,7 +45,8 @@ extensions = [
'sphinx.ext.coverage',
'sphinx.ext.mathjax',
'sphinx.ext.viewcode',
'sphinx.ext.autosummary'
'sphinx.ext.autosummary',
'sphinxcontrib.bibtex'
]
# Add any paths that contain templates here, relative to this directory.
......
......@@ -13,15 +13,49 @@ Welcome to Peppa-PIG's documentation!
What is Peppa-PIG ?
===================
Peppa-PIG is python package to impute missing SNP summary statistics from
neighborring SNPs in linkage desiquilibrium.
The statistical model used to make the imputation is described in :cite:`Pasaniuc2014`
Dependancies
============
peppa-pig require plink version
Peppa-PIG require plink version 1.9
Installation
============
.. code-block:: shell
pip3 install git+https://gitlab.pasteur.fr/statistical-genetics/imputation_for_jass
Precomputation of LD-correlation
=================================
The imputation is based the Linkage desiquilibrium between SNPs.
To save computation the LD is computed and saved perform the imputation is
performed. To limit the number of SNP pairs, the LD is computed between SNPs in
region of approximately LD-independant. For an european ancestry, you can use
the region defined by Berisa.
To compute the LD you need to specify a reference panel (bed, fam and bim
formats of plink, see `PLINK formats <https://www.cog-genomics.org/plink2/formats>` )
.. code-block:: python
for i in 1:22:
impute_jass.LD.launch_plink_ld(start,stop,...)
Launching imputation on one chromosome
======================================
Peppa-PIG has an interface with the command line.
If you have access to a cluster, an efficient way to use Peppa-PIG is to launch
the imputation of each chromosome on a separate cluster nude
Indices and tables
==================
......@@ -35,3 +69,5 @@ Indices and tables
.. autosummary::
:toctree: _autosummary
.. bibliography:: reference.bib
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