relexprByGene {casper}R Documentation

Compute relative expressions within each gene

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)

[Package casper version 2.26.0 Index]