rpkmToTpm: Converts RPKM or FPKM estimates to TPM. Per Colin Dewey,

In RamsinghLab/arkas_staging: A package that complements Kallisto for quick, informative *seq analysis

Description

tpm[i, j] == (rpkm[i, j]/(sum(rpkm[i, ]))) * 1e6

Usage

rpkmToTpm(rpkm, ...)

.tpmBySample(rpkm)

Arguments

rpkm	a matrix of RPKM or FPKM estimates
...	any additional user input arguments

Details

For nonzero rpkm, this becomes

tpm[i, nonzero] == exp( log(rpkm[i, nonzero]) - log(sum(rpkm[i, nonzero])) + log(1e6) )

and of course if RPKM == 0 then TPM == 0 as well.

Value

a matrix of TPM estimates

Functions

• .tpmBySample:

See Also

http://bioinformatics.oxfordjournals.org/content/26/4/493.full

RamsinghLab/arkas_staging documentation built on March 14, 2021, 11:40 a.m.