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drigodwin/gist:07d8bbdb81ae2de6e35afa663098799f

Last active October 12, 2017 10:48
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gistfile1.txt
tpm <- function(counts, lengths) {
rate <- counts / lengths
rate / sum(rate) * 1e6
}
ftr.cnt <- read.table("counts.txt", sep="\t", stringsAsFactors=FALSE,
header=TRUE)
library(dplyr)
library(tidyr)
ftr.tpm <- ftr.cnt %>%
gather(sample, cnt, 3:ncol(ftr.cnt)) %>%
mutate(tpm=tpm(cnt, Length)) %>%
select(-cnt) %>%
spread(sample, tpm)
write.table(ftr.tpm, file=tpm.esc.txt, sep="\t", row.names=FALSE, quote=FALSE)
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