getGenes: getGenes

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

Description

Primary accessor from a CuffSet object to retrive all related information for >1 (MANY) given genes, indexed by gene_id or gene_short_name.

Usage

## S4 method for signature 'CuffSet'
getGenes(object, geneIdList, sampleIdList=NULL)

Arguments

object	An object of class 'CuffSet' (Primary 'pointer' object for Cufflinks data).
geneIdList	A vector of gene_ids or gene_short_namesto identify which genes for which you would like to retrieve all information.
sampleIdList	A vector of sample names used to subset or re-order samples in returned object

Details

None.

Value

Returns a CuffGeneSet object containing all related information for a given set of gene_id or gene_short_name values

Note

Right now, this does not return an error if it cannot find a gene. (this is probably a bad thing...)

Author(s)

Loyal A. Goff

References

None.

Examples

	a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data and create master CuffSet object
	data(sampleData)
	sampleIDs
	myGene<-getGenes(a,sampleIDs) # Retrieve all information for a set of 20 'sample' genes.

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