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saving work before adding files

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Tanushree Tunstall 2021-06-18 17:47:09 +01:00
parent 86ed1805fc
commit f6a2e029cb
3 changed files with 47 additions and 24 deletions
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17
scripts/af_or_calcs.R
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@ -20,14 +20,14 @@ source("functions/myaf_or_calcs.R")
# command line args
#********************
spec = matrix(c(
"drug" ,"d" , 1, "character",
"gene" ,"g" , 1, "character",
"master_data" ,"m", 2, "character",
"gene_data" ,"G", 2, "character",
"outfile" ,"o" , 2, "character",
"idcol" ,"I", 2, "character",
"drmuts_col" ,"D", 2, "character",
"othermuts_col" ,"O", 2, "character"
"drug" ,"d", 1, "character",
"gene" ,"g", 1, "character",
"master_data" ,"m", 2, "character",
"gene_data" ,"G", 2, "character",
"outfile" ,"o", 2, "character",
"idcol" ,"I", 2, "character",
"drmuts_col" ,"D", 2, "character",
"othermuts_col" ,"O", 2, "character"
), byrow = TRUE, ncol = 4)
@ -109,7 +109,6 @@ if (is.null(other_muts_col)){
other_muts_col
cat("\ndrug and other mut colnames not specified, sourcing from globals: "
, other_muts_col, "\n")
}
# Informing the user of the sensible defaults being used: