Closed karissawhiting closed 1 year ago
@karissawhiting
add_pathways identifies columns for .mut with regular expressions using stringr
this might mess up the function because it identified sample_id as a mut_col, should be an easy fix by adding in sample_id to the str_detect()
all_cols <- colnames(gene_binary)
mut_cols <- !(str_detect(all_cols, ".Amp|.Del|.fus|.cna"))
custom_pathways <- purrr::map(custom_pathways, function(x) {
x[!str_detect(x, ".Amp|.Del|.fus|.cna")] <-
paste0(stringr::str_trim(
x[!str_detect(x, ".Amp|.Del|.fus|.cna")]), ".mut")
unique(x)
} )
@karissawhiting @hfuchs5 I am going to make another pr/branch for this after we merge in the changes from internal_gen_bin_tidy bc those are the changes that will affect this
Related to changes in #177