Commit 83bf40d8 authored by Hanna  JULIENNE's avatar Hanna JULIENNE
Browse files

fix table and install jass_preprocessing in .yml

parent 7e207267
Pipeline #18990 passed with stages
in 59 seconds
......@@ -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
......
......@@ -40,7 +40,7 @@ The QC and preprocessing step goes as follow:
+-------+-----------+--------+----+----+-----+-----+
| chrom | rsID | pos | A0 | A1 | Z | P |
+-------+-----------+--------+----+----+-----+-----+
| 1 | rs4075116 |1003629 | C | T |0.30 | 0.76|
| 1 | rs4075116 |1003629 | C | T | 0.3 | 0.76|
+-------+-----------+--------+----+----+-----+-----+
......@@ -79,15 +79,15 @@ Input
* the fields are:
+-------------------------------------------+------------------------------------------------------------+
+-------------------------------------------+---------------------------------------------------------------+
| category | field name |
+===========================================+============================================================+
+===========================================+===============================================================+
| path to the data | filename |
+-------------------------------------------+------------------------------------------------------------+
| study info fields | Consortium,Outcome,fullName,type,Nsample,Ncase,Ncontrol,Nsnp|
+-------------------------------------------+------------------------------------------------------------+
+-------------------------------------------+---------------------------------------------------------------+
| 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|
......@@ -117,6 +117,6 @@ Indices and tables
* :ref:`genindex`
* :ref:`modindex`
.. automodule:: impute_jass
.. automodule:: jass_preprocessing
:members:
* :ref:`search`
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