Nothing
subDose <- function(file=NULL, vmmk=NULL, out=NULL, removeInsertions=TRUE, verbose=TRUE){
# Avoid E-Notation
options("scipen"=100, "digits"=4)
# Basic input check
if(is.null(file)) stop("No *.dose file given.")
if(is.null(vmmk)) stop("No Variant-Map-Master-Key file given.")
if(is.null(out)) out <- paste("Allele-",file,sep="")
# Read in the variant master key:
master <- read.table(vmmk, stringsAsFactors=FALSE)
# Read in the dose file
dose <- read.table(file, header=TRUE, stringsAsFactors=FALSE)
# Output
if(verbose) cat("I read the dose file and the VMMK.",date(),"\n")
# Check if the order is correct, otherwise stop the script!
if(sum(dose$marker==master$V1)!=nrow(dose)) stop("The order does not match between the files")
# Now change the dose table
dose$alleleA <- master$V3
dose$alleleB <- master$V4
# Remove the Insertions
if(removeInsertions) dose <- dose[-which(master$V7=="I"),]
# write out the new Dose file
write.table(dose,out, col.names=TRUE, row.names=FALSE, quote=FALSE)
}
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