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morinlab / GAMBLR

Set of standardized functions to operate with genomic data
https://morinlab.github.io/GAMBLR/
MIT License
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get_ssm_by_region incorrectly subsets on five columns, regardless if basic_column is TRUE #97

Closed mattssca closed 1 year ago

mattssca commented 2 years ago

This function needs to be updated so that all MAF columns are retained.

Currently, the function subsets on Chromosome, Start_Position, End_Position, Tumor_Sample_Barcode and Read_Support when reading indexed maf. Thus, using basic_columns = TRUE cannot subset on columns 1-45 throws an error.

This function can possibly be simplified using the Vroom package to read data into R.

rdmorin commented 1 year ago

I think I've gotten this issue sorted out now (waiting on the PR to get into Master).