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Statistical-Genetics
jass_preprocessing
Commits
83bf40d8
Commit
83bf40d8
authored
Nov 28, 2019
by
Hanna JULIENNE
Browse files
fix table and install jass_preprocessing in .yml
parent
7e207267
Pipeline
#18990
passed with stages
in 59 seconds
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2
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.gitlab-ci.yml
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83bf40d8
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@@ -15,7 +15,7 @@ pages:
-
pip3 install sphinx
-
pip3 install sphinxcontrib-bibtex sphinx_rtd_theme sphinx-argparse
-
pip3 install -r requirements.txt
-
pip3 install
pandas
-
pip3 install
../jass_preprocessing/
-
cd doc
-
sphinx-apidoc -f -o ./source/_autosummary/ ../jass_preprocessing/
-
make html
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doc/source/index.rst
View file @
83bf40d8
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@@ -38,9 +38,9 @@ The QC and preprocessing step goes as follow:
(input format needed to perform LD-score)
+-------+-----------+--------+----+----+-----+-----+
| chrom | rsID | pos | A0
| A1 | Z |
P
|
| chrom | rsID | pos | A0
| A1 | Z |
P
|
+-------+-----------+--------+----+----+-----+-----+
| 1
| rs4075116 |1003629 | C | T
|0.3
0
| 0.76|
| 1 | rs4075116 |1003629 | C | T
|
0.3 | 0.76|
+-------+-----------+--------+----+----+-----+-----+
...
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@@ -79,22 +79,22 @@ Input
* the fields are:
+-------------------------------------------+------------------------------------------------------------+
| category | field name |
+===========================================+============================================================+
| path to the data | filename |
+-------------------------------------------+------------------------------------------------------------+
| study info fields | Consortium,Outcome,fullName,type,Nsample,Ncase,Ncontrol,Nsnp|
+-------------------------------------------+------------------------------------------------------------+
| names of the header in the GWAS file | snpid,a1,a2,freq,pval,n,z,OR,se,code,imp,ncas,ncont |
+-------------------------------------------+------------------------------------------------------------+
+-------------------------------------------+------------------------------------------------------------
---
+
| category |
field name |
+===========================================+============================================================
===
+
| path to the data | filename
|
+-------------------------------------------+------------------------------------------------------------
---
+
| study info fields | Consortium,Outcome,fullName,type,Nsample,Ncase,Ncontrol,Nsnp
|
+-------------------------------------------+------------------------------------------------------------
---
+
| names of the header in the GWAS file | snpid,a1,a2,freq,pval,n,z,OR,se,code,imp,ncas,ncont
|
+-------------------------------------------+------------------------------------------------------------
---
+
.. Give an example
.. | I don't know | altNcas,altNcont|
Note that the combination of Consortium and outcome must be unique because it will be used as an index in the cleaning process.
Here is an example of descriptor field, the field irrelevant (for example odd ratio for continuous trait) for the study must be filled with na.
Here is an example of descriptor field, the field irrelevant (for example odd ratio for continuous trait) for the study must be filled with na.
.. csv-table:: GWAS information table!
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@@ -117,6 +117,6 @@ Indices and tables
* :ref:`genindex`
* :ref:`modindex`
.. automodule::
impute_jass
.. automodule::
jass_preprocessing
:members:
* :ref:`search`
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