#normalize as used for RNA seq with 1.1 added to avoid zeroes, round to tenths
args <- commandArgs(trailingOnly = TRUE)
intab <- args[1]
outtab <- args[2]
data <- read.table(intab, sep="\t", header=TRUE, row.names=1)
#quantile
library(limma)
limmaRes = normalizeQuantiles(data)
log.lres = round(log2(limmaRes + 1.1), digits=1)
write.table(log.lres, file=outtab, row.names = TRUE ,col.names = TRUE,quote = FALSE, sep="\t")