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#!/usr/bin/env Rscript
################################################
# for info on upper quartile normalization, see:
# http://vinaykmittal.blogspot.com/2013/10/fpkmrpkm-normalization-caveat-and-upper.html
################################################
suppressPackageStartupMessages(library("argparse"))
parser = ArgumentParser()
parser$add_argument("--matrix", help="input data file", required=TRUE, nargs=1)
parser$add_argument("--output", help="output data file", required=TRUE, nargs=1)
args = parser$parse_args()
matrix_filename = args$matrix
output_filename = args$output
data = read.table(gzfile(matrix_filename), header=T, sep="\t", row.names=1, check.names=F, com='')
get_upper_quartile = function(vec) {
vec = vec[vec > 0]
quantile(vec, 0.75)
}
data = as.matrix(data)
upp_quartiles = apply(data, 2, get_upper_quartile)
m = sweep(data, MARGIN=2, upp_quartiles, '/')
mean_upp_quart = mean(upp_quartiles)
m = m * mean_upp_quart
write.table(m, file=output_filename, quote=F, sep="\t", col.names=NA)
quit(save = "no", status = 0, runLast = FALSE)
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