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aehrc / VariantSpark

machine learning for genomic variants
http://bioinformatics.csiro.au/variantspark
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Update the Cloud Marketplace example Notebooks to include logistic regression covariates #192

Open BauerLab opened 3 years ago

piotrszul commented 3 years ago

@BauerLab as far as I can tell they are already included in the example notebook see: https://bitbucket.csiro.au/users/hos076/repos/variantspark-aws/browse/data/monitor-ami/notebook/VariantSpark_example.ipynb (or : https://variantspark-marketplace-resources.s3.amazonaws.com/static/public/example_notebook.html)

covariates = [mt.pheno.isFemale, mt.pcs[0], mt.pcs[1]]

result = hl.logistic_regression_rows(test ='wald', 
                                          y=mt.pheno.isCase,
                                          x=mt.GT.n_alt_alleles(),
                                          covariates=covariates)

Also as the code for AWS deployment is managed in different repository I think it would be better to manage the related issue somewhere else, unless they do require changes in the core variant spark.