getGeneId: getGene

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

View source: R/methods-CuffSet.R

Description

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

Usage

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

Arguments

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.

Details

None.

Value

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

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

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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.

cummeRbund documentation built on Nov. 17, 2017, 1:40 p.m.