countsToTPM: Convert a numeric matrix of features (rows) and conditions...

In richysix/rnaseqtools: Helpers for dealing with our RNA-seq output

Convert a numeric matrix of features (rows) and conditions (columns) with raw feature counts to transcripts per million.

Description

This function is from https://gist.github.com/slowkow/c6ab0348747f86e2748b#file-counts_to_tpm-r Convert counts to transcripts per million (TPM).

Usage

countsToTPM(counts, featureLength, meanFragmentLength)

Arguments

counts	A numeric matrix of raw feature counts i.e. fragments assigned to each gene.
featureLength	A numeric vector with feature lengths. This should be the same length as the number of features
meanFragmentLength	A numeric vector with mean fragment lengths. This should be the same length as the number of samples

Details

Lior Pachter. Models for transcript quantification from RNA-Seq. arXiv:1104.3889v2

Wagner, et al. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci. 24 July 2012. doi:10.1007/s12064-012-0162-3

Value

tpm A numeric matrix normalized by library size and feature length

Examples

set.seed(1785)
counts <- matrix(sample(20:200, size = 100), ncol = 5)
featureLength <- sample(200:1000, size = 20)
meanFragmentLength <- sample(200:300, size = 5)
countsToTPM(counts, featureLength, meanFragmentLength)

richysix/rnaseqtools documentation built on Jan. 26, 2025, 10:14 a.m.