- Quick and dirty fix to adding "additional variables" when also running fillouts. Currently will only work with ONE additional variable.
- If one MAF has clonality and the other DOESNT and you are running fillouts, on return to performance scripts the script will think that clonality/purity exists in BOTH mafs because fillouts returns the merged results.... Look below for where the issue is. need to think of some better logic
404 colnames(ground_tmp)[grepl("^t_", colnames(ground_tmp))] <- paste0(colnames(ground_tmp)[grepl("^t_", colnames(ground_tmp))], "_called_ground") 405 colnames(test_tmp)[grepl("^t_", colnames(test_tmp))] <- paste0(colnames(test_tmp)[grepl("^t_", colnames(test_tmp))], "_called_test") 406 # colnames(test_tmp)[colnames(test_tmp) %nin% colnames(ground_tmp)] <- paste0( colnames(test_tmp)[colnames(test_tmp) %nin% colnames(ground_tmp)],"_test_col") 407 ground_tmp[, "t_ref_count"] <- ground$t_ref_count 408 ground_tmp[, "t_alt_count"] <- ground$t_alt_count 409 fillout_maf <- merge(ground_tmp, test_tmp[test_tmp$var_tag %in% shared_variants, c("var_tag", colnames(test_tmp)[colnames(test_tmp) %nin% colnames(ground_tmp)])], by = "var_tag", 410 all.x = TRUE) 411 test_tmp <- test_tmp[test_tmp$var_tag %nin% shared_variants, ] 412 fillout_maf <- bind_rows(fillout_maf, test_tmp) 413 414 415 fillout_maf[is.na(fillout_maf$Called_in_Ground), "Called_in_Ground"] <- TRUE 416 fillout_maf[is.na(fillout_maf$Called_in_Test), "Called_in_Test"] <- TRUE
Theres a specail issues with DMP vs TEMPO where they each have Protein_Position in the colnames, making the bind to make a unified MAF for fillouts problematic. Right now I have a bandaid for the issue, but once again it is related to the above logic ^^^.
Theres a specail issues with DMP vs TEMPO where they each have Protein_Position in the colnames, making the bind to make a unified MAF for fillouts problematic. Right now I have a bandaid for the issue, but once again it is related to the above logic ^^^.