Update ibdreduce_v3.py to allow for a matrix phenotype file or 2 column file#32
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rjbohlender merged 1 commit intomasterfrom Sep 28, 2025
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Refactoring of the parse_pheno function in ibdreduce so that the user can select a column from a phecode matrix to use as the phenotype
jtb324
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Feature(ibdreduce_v3.py):
Refactoring of the parse_pheno function in ibdreduce so that the user can select a column from a phecode matrix to use as the phenotype.
What was added:
Description:
This commit addresses issue #31. The user can now provide either a 2 column phenotype file or they can provide a matrix file with many columns. If the matrix is provided then they also should provide the phenotype name as an argument so that the parse_pheno function will select the right column from the matrix (lines 180-184). If the user passes a 2 column file then the program defaults to normal behavior. This commit adds convenience for people who already have a matrix style file from PheWAS analyses, etc...