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Statistical-Genetics
RAISS
Commits
eab6512c
Commit
eab6512c
authored
Nov 25, 2018
by
hjulienne
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add command line usage documentation
parent
00b4450b
Pipeline
#7850
passed with stages
in 1 minute and 13 seconds
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5 changed files
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30 additions
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18 deletions
+30
-18
.gitlab-ci.yml
.gitlab-ci.yml
+2
-2
impute_jass/doc/source/conf.py
impute_jass/doc/source/conf.py
+3
-2
impute_jass/doc/source/index.rst
impute_jass/doc/source/index.rst
+20
-12
impute_jass/impute_jass/__main__.py
impute_jass/impute_jass/__main__.py
+4
-2
impute_jass/setup.py
impute_jass/setup.py
+1
-0
No files found.
.gitlab-ci.yml
View file @
eab6512c
...
...
@@ -13,7 +13,7 @@ pages:
-
pip3 install sphinx
-
yum install -y make
-
pip3 install sphinx
-
pip3 install sphinxcontrib-bibtex
-
pip3 install sphinxcontrib-bibtex
sphinx_rtd_theme sphinx-argparse
-
pip3 install -r impute_jass/requirements.txt
-
cd impute_jass/doc
-
make html
...
...
@@ -22,4 +22,4 @@ pages:
paths
:
-
public
only
:
-
master
\ No newline at end of file
-
master
impute_jass/doc/source/conf.py
View file @
eab6512c
...
...
@@ -46,7 +46,8 @@ extensions = [
'sphinx.ext.mathjax'
,
'sphinx.ext.viewcode'
,
'sphinx.ext.autosummary'
,
'sphinxcontrib.bibtex'
'sphinxcontrib.bibtex'
,
'sphinxarg.ext'
]
# Add any paths that contain templates here, relative to this directory.
...
...
@@ -82,7 +83,7 @@ pygments_style = 'sphinx'
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
html_theme
=
'
bizstyl
e'
html_theme
=
'
sphinx_rtd_them
e'
# 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
...
...
impute_jass/doc/source/index.rst
View file @
eab6512c
...
...
@@ -4,7 +4,7 @@
contain the root `toctree` directive.
Welcome to the Robust and Accurate Imputation from Summary Statistics (RAISS) documentation!
=====================================
=====================================
=======================================================
.. toctree::
:maxdepth: 2
...
...
@@ -13,8 +13,8 @@ Welcome to the Robust and Accurate Imputation from Summary Statistics (RAISS) do
What is RAISS ?
===================
RAISS is python package to impute missing SNP summary statistics from
neighbor
r
ing SNPs in linkage desiquilibrium.
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`
...
...
@@ -35,15 +35,16 @@ Installation
Precomputation of LD-correlation
=================================
The imputation is based the Linkage desiquilibrium between SNPs.
The imputation is based the Linkage desiquilibrium
between SNPs.
To save computation t
he LD is computed and saved perform the imputation is
performed.
To limit the number of SNP pairs, the LD is computed between pairs of
To save computation t
ime, the LD is computed before imputation and saved as tabular format.
To limit the number of SNP pairs, the LD is computed between pairs of
SNPs in a approximately LD-independent regions. For an european ancestry, you can use
the region defined by :cite:`Berisa2015` that are provided in the package data folder.
To compute the LD you need to specify a reference panel splitted by chromosomes
(bed, fam and bim formats of plink, see `PLINK formats <https://www.cog-genomics.org/plink2/formats>` )
(bed, fam and bim formats of plink, see `PLINK formats <https://www.cog-genomics.org/plink2/formats>`
_
)
.. code-block:: python
...
...
@@ -59,7 +60,6 @@ To compute the LD you need to specify a reference panel splitted by chromosomes
Input format:
=============
GWAS results files must be provided in the tabular format by chromosome (tab separated)
all in the same folder with the following columns with the same header:
...
...
@@ -69,13 +69,13 @@ all in the same folder with the following columns with the same header:
| rs6548219| 30762 | A | G | -1.133 |
+----------+-------+------+-----+--------+
This format can be obtain with the `JASS PreProcessing package <https://gitlab.pasteur.fr/statistical-genetics/JASS_Pre-processing>`.
This format can be obtain
ed
with the `JASS PreProcessing package <https://gitlab.pasteur.fr/statistical-genetics/JASS_Pre-processing>`.
Launching imputation on one chromosome
======================================
RAISS has an interface with the command line.
RAISS has an interface with the command line
(see Command Line Usage bellow)
.
If you have access to a cluster, an efficient way to use RAISS is to launch
the imputation of each chromosome on a separate cluster node. The script
...
...
@@ -88,6 +88,7 @@ Output
The raiss package outputs imputed GWAS files in the tabular format:
#TODO suppress complementary columns
+------------+---+--+----------------+-----+-----+----------------+------------------+---------+---------+
| |A0 |A1| Nsnp_to_impute |Var |Z |condition_number|correct_inversion |ld_score | pos |
+============+===+==+================+=====+=====+================+==================+=========+=========+
...
...
@@ -96,18 +97,25 @@ The raiss package outputs imputed GWAS files in the tabular format:
# Keep only useful columns
Command Line Usage
==================
.. argparse::
:ref: impute_jass.__main__.add_chromosome_imputation_argument
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
.. automodule:: impute_jass
:members:
* :ref:`search`
.. autosummary::
:toctree: _autosummary
.. bibliography:: reference.bib
impute_jass/impute_jass/__main__.py
View file @
eab6512c
...
...
@@ -32,7 +32,9 @@ def launch_chromosome_imputation(args):
imputed_zscore
.
to_csv
(
z_fo
,
sep
=
'
\t
'
)
print
(
"Save imputation done at {0}"
.
format
(
z_fo
))
def
add_chromosome_imputation_argument
(
parser
):
def
add_chromosome_imputation_argument
():
parser
=
argparse
.
ArgumentParser
()
parser
.
add_argument
(
'--chrom'
,
required
=
True
,
help
=
"chromosome to impute to the chr\d+ format"
)
parser
.
add_argument
(
'--gwas'
,
required
=
True
,
help
=
"GWAS to impute to the consortia_trait format"
)
...
...
@@ -50,7 +52,7 @@ def add_chromosome_imputation_argument(parser):
def
main
():
parser
=
argparse
.
ArgumentParser
()
#prog='impute_jass')
#prog='impute_jass')
parser
=
add_chromosome_imputation_argument
(
parser
)
args
=
parser
.
parse_args
()
args
.
func
(
args
)
...
...
impute_jass/setup.py
View file @
eab6512c
...
...
@@ -9,6 +9,7 @@ setup(name='impute_jass',
license
=
'MIT'
,
#package_dir = {'': 'jass_preprocessing'},
packages
=
[
'impute_jass'
],
package_data
=
{
'impute_jass'
:
'./data/*.csv'
},
zip_safe
=
False
,
...
...
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