mc.sortByChromosom <- function(mutnet.obj, col.chrom= "chrom", col.pos="pos"){
mutnet.obj[,col.pos] <- as.numeric(mutnet.obj[,col.pos])
mutnet.obj[, col.chrom] <- as.character(mutnet.obj[, col.chrom])
chromosomes <- unique(mutnet.obj[,col.chrom])
max.num <- max(as.numeric(chromosomes[grepl("\\d", chromosomes)]))
s.1 <- which(mutnet.obj[,col.chrom] == "X")
s.2 <- which(mutnet.obj[,col.chrom] == "Y")
mutnet.obj[s.1, col.chrom] <- max.num+1
mutnet.obj[s.2, col.chrom] <- max.num+2
# other chromosomes to NA
mutnet.obj[!grepl("\\d", mutnet.obj[, col.chrom]), col.chrom] <- NA
mutnet.obj[, col.chrom] <- as.numeric(mutnet.obj[,col.chrom])
o <- order(mutnet.obj[,col.chrom], mutnet.obj[,col.pos], na.last=TRUE)
mut.sort <- mutnet.obj[o,]
return(mut.sort)
}
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