totalGeneCounts: Auxiliary function to build gene expression matrix

In gamerino/NBSplice: Negative Binomial Models to detect Differential Splicing

Description

totalGeneCounts obtains the total counts for a gene in a sample by the sum of the counts of all its isoforms. This count is performed before any filter step to avoid erroneus estimation of isoform ratios.

Usage

totalGeneCounts(isoCounts, geneIso, BPPARAM = bpparam())

Arguments

isoCounts	Matrix containing the isoform expression values with isoforms in rows and samples in columns. Object row names should be the names of the isoforms and the column names, the names of each sample.
geneIso	Data.frame with two columns called "isoform_id" and "gene_id" especifying which are the isoform (rows of the expression matrix) for each gene
BPPARAM	A bpparam object specifying the number of cpus to be used.

Value

A matrix of the same size as the isoCounts matrix with the total counts for each gene in each sample in CPM scale.

Author(s)

Gabriela A. Merino [e-mail] and Elmer A. Fernandez [e-mail]

Examples

data(isoCounts, package="NBSplice")
data(geneIso, package="NBSplice")

myGeneCounts<-totalGeneCounts(isoCounts, geneIso)

gamerino/NBSplice documentation built on Sept. 10, 2021, 10:21 p.m.