getGeneId: getGene

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

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

## 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

	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.

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