Add command line option for sample overlap to mutation prediction scripts #43
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miltondp
approved these changes
Apr 22, 2021
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Closes #33.
In our paper, we want to compare data types for mutation prediction in 3 different experiments: one using gene expression data only, one using gene expression and methylation, and one using expression/methylation/RPPA/mutational signatures data. In each of these cases, we only want to use TCGA samples that have data for all of these data types.
Before, I was handling this in a super hacky way, by commenting out lines in
mpmp/config.py. This change creates a command line option to select the data types to use for calculating the sample overlap, which makes this step much more reproducible and understandable.It's a fairly straightforward change to the code, not too much to review.