totalGeneCounts: Auxiliary function to build gene expression matrix

Description Usage Arguments Value Author(s) Examples

View source: R/totalGeneCounts.R

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

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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 merino.gabriela33@gmail.com and Elmer A. Fernandez efernandez@bdmg.com.ar

Examples

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

myGeneCounts<-totalGeneCounts(isoCounts, geneIso)

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