countTableForGene {DEXSeq}R Documentation

Count table for a given geneID.

Description

This function returns a matrix of non negative integers containing a count table for a specified geneID from an ExonCountSet object. The count table contains one row for every counting bin of the gene and a column for every sample.

Usage

countTableForGene(ecs, geneID, normalized=FALSE, withDispersion=FALSE)

Arguments

ecs

An ExonCountSet.

geneID

A geneID to get the count table.

normalized

If TRUE, the raw counts will be normalized by the size factors.

withDispersion

If TRUE, an extra column with the dispersion estimate used in the test will added to the count table.

See Also

estimateSizeFactors

Examples

   data("pasillaExons", package="pasilla")
   pasillaExons <- estimateSizeFactors( pasillaExons )
   countTableForGene(pasillaExons, "FBgn0085442", normalized=FALSE)

[Package DEXSeq version 1.0.2 Index]