relexprByGene: Compute relative expressions within each gene

In casper: Characterization of Alternative Splicing based on Paired-End Reads

Description

Transforms relative expressions that add up to 1 within each gene island (the default output of casper) to relative expressions that add up to 1 per gene.

Usage

relexprByGene(x, normbylength=FALSE, genomeDB)

Arguments

x	ExpressionSet containing relative expressions. (typically, adding up to 1 for each island_id) Column gene_id in fData(x) should contain a unique gene identifier.
normbylength	If set to TRUE, isoform expressions are divided by isoform length before re-normalizing. This is useful for taking into account that longer isoforms produce more reads than shorter isoforms.
genomeDB	If normbylength==TRUE, genomeDB should be an annotatedGenome object containing the annotated genome (see procGenome)

Value

ExpressionSet with relative expressions adding up to one for each gene_id.

Author(s)

David Rossell

Examples

#See help(calcExp)

casper documentation built on Dec. 17, 2020, 2:01 a.m.