getGeneId: getGene
In cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

Description Usage Arguments Details Value Note Author(s) References Examples

A helper function to retrieve the gene_ids for a given list of feature ids (e.g. isoform_ids, tss_group_ids, or CDS_ids). This should not be called directly by the user

1 2	## S4 method for signature 'CuffSet' getGeneId(object, idList)

`object`	An object of class 'CuffSet' (Primary 'pointer' object for Cufflinks data).
`idList`	A character string to identify the identifiers for which you would like to retrieve corresponding gene_id values.

None.

Returns a vector of gene_id values corresponding to genes from which idList are sub-features.

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

Loyal A. Goff

None.

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	cuff<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data and create master CuffSet object
	sampleFeatureIds<-sample(featureNames(isoforms(cuff)),10)
	correspondingGeneIds<-getGeneId(cuff,sampleFeatureIds) # Retrieve gene_id values for parent genes of sampleFeatureIds.