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: ...@@ -15,7 +15,7 @@ pages:
- pip3 install sphinx - pip3 install sphinx
- pip3 install sphinxcontrib-bibtex sphinx_rtd_theme sphinx-argparse - pip3 install sphinxcontrib-bibtex sphinx_rtd_theme sphinx-argparse
- pip3 install -r requirements.txt - pip3 install -r requirements.txt
- pip3 install pandas - pip3 install ../jass_preprocessing/
- cd doc - cd doc
- sphinx-apidoc -f -o ./source/_autosummary/ ../jass_preprocessing/ - sphinx-apidoc -f -o ./source/_autosummary/ ../jass_preprocessing/
- make html - make html
......
...@@ -38,9 +38,9 @@ The QC and preprocessing step goes as follow: ...@@ -38,9 +38,9 @@ The QC and preprocessing step goes as follow:
(input format needed to perform LD-score) (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 |0.30 | 0.76| | 1 | rs4075116 |1003629 | C | T | 0.3 | 0.76|
+-------+-----------+--------+----+----+-----+-----+ +-------+-----------+--------+----+----+-----+-----+
...@@ -79,22 +79,22 @@ Input ...@@ -79,22 +79,22 @@ Input
* the fields are: * the fields are:
+-------------------------------------------+------------------------------------------------------------+ +-------------------------------------------+---------------------------------------------------------------+
| category | field name | | category | field name |
+===========================================+============================================================+ +===========================================+===============================================================+
| path to the data | filename | | 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 | | names of the header in the GWAS file | snpid,a1,a2,freq,pval,n,z,OR,se,code,imp,ncas,ncont |
+-------------------------------------------+------------------------------------------------------------+ +-------------------------------------------+---------------------------------------------------------------+
.. Give an example .. Give an example
.. | I don't know | altNcas,altNcont| .. | 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. 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! .. csv-table:: GWAS information table!
...@@ -117,6 +117,6 @@ Indices and tables ...@@ -117,6 +117,6 @@ Indices and tables
* :ref:`genindex` * :ref:`genindex`
* :ref:`modindex` * :ref:`modindex`
.. automodule:: impute_jass .. automodule:: jass_preprocessing
:members: :members:
* :ref:`search` * :ref:`search`
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment