diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 0d224963eeaf2409555bd0d5de3e94ebd3cf65a5..b77bc85e2ef9bb1b4fc5784872889665ab787c93 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -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 diff --git a/doc/source/index.rst b/doc/source/index.rst index 83387d811424fce8607e4741070f08c1c1c48550..0f6b594cbf10b40b6636a20e6f0c80d98774d00c 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -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 |0.30 | 0.76| +| 1 | rs4075116 |1003629 | C | T | 0.3 | 0.76| +-------+-----------+--------+----+----+-----+-----+ @@ -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! @@ -117,6 +117,6 @@ Indices and tables * :ref:`genindex` * :ref:`modindex` -.. automodule:: impute_jass +.. automodule:: jass_preprocessing :members: * :ref:`search`