getFeatures: getFeatures

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

Description

Primary accessor from a CuffSet object to retrieve all related information for >1 (MANY) given FEATURES, indexed by tracking id.

Usage

## S4 method for signature 'CuffSet'
getFeatures(object, featureIdList, sampleIdList=NULL,level='isoforms')

Arguments

object	An object of class 'CuffSet' (Primary 'pointer' object for Cufflinks data).
featureIdList	A vector of 'isoform_id', 'TSS_group_id', or 'CDS_id' to identify which features 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
level	Feature level to be queried for significance (must be one of c('isoforms','TSS','CDS')

Details

None.

Value

Returns a CuffFeatureSet object containing all related information for a given set of tracking_id 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

	cuff<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data and create master CuffSet object
	sample.isoform.ids<-sample(featureNames(isoforms(cuff)),10)
	myGene<-getFeatures(cuff,sample.isoform.ids) # Retrieve all information for a set of 10 sampled features.

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