countMatrix: countMatrix

In gofflab/cummeRbund-BioC-Bridge: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

Description

Retrieve count values as gene by condition matrix

Usage

## S4 method for signature 'CuffData'
countMatrix(object,fullnames=FALSE,sampleIdList)
## S4 method for signature 'CuffData'
repCountMatrix(object,fullnames=FALSE,repIdList)

Arguments

object	An object of class ('CuffData','CuffFeatureSet','CuffGeneSet','CuffGene',or 'CuffFeature')
fullnames	A logical value whether or not to concatenate gene_short_name and tracking_id values (easier to read labels)
sampleIdList	A vector of sample names to subset the resulting matrix.
repIdList	A vector of replicate names to subset the resulting replicate matrix.

Details

None.

Value

A feature x condition matrix of count values.

Note

None

Author(s)

Loyal A. Goff

References

None.

Examples

	data(sampleData)
	countMatrix(sampleGeneSet)
	repCountMatrix(sampleGeneSet)

gofflab/cummeRbund-BioC-Bridge documentation built on May 17, 2019, 7:30 a.m.