get_TPM {granulator}R Documentation

Convert raw counts to TPM

Description

get_TPM is used to convert raw counts to TPMs, which is the most suitable normalization for deconvolution.

Usage

get_TPM(counts, effLen)

Arguments

counts

Bulk RNAseq: a genes (rows) by samples (columns) matrix containing gene raw counts.

effLen

Vector of gene lengths.

Value

Returns a transcript-per-million (TPM)-normalized matrix.

Author(s)

Vincent Kuettel, Sabina Pfister

Examples

# get TPMs from raw counts and gene lengths.
mat <- round(matrix(rexp(200, rate=.01), ncol=20))
len <- round(matrix(rexp(10, rate=.001), ncol=1))+10
tpm <- get_TPM(mat,as.vector(len))


[Package granulator version 1.2.0 Index]