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In this PR:
analyze.pgs.binary.predictivenesswhich given a PGS and phenotypes runs a logistic regression and returns statistics (OR, p-value, AUC) describing how well the PGS predicts the phenotype. It also automatically plots a receiver-operator-curve.I have read the code review guidelines and the code review best practice on GitHub check-list.
The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)-[brief_description_of_branch].
I have set up or verified the branch protection rule following the github standards before opening this pull request.
I have added the changes included in this pull request to
NEWSunder the next release version or unreleased, and updated the date.I have updated the version number in
metadata.yamlandDESCRIPTION.Both
R CMD buildandR CMD checkrun successfully.Testing Results
All unit tests PASS
Also R CMD check passes locally where scales is installed.
The CICD check fails because scales is not installed in the image and since it is a suggested dependency it is not automatically installed by the package.