getSig: getSig

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

Description

Returns the identifiers of significant genes in a vector format.

Usage

## S4 method for signature 'CuffSet'
getSig(object,x,y,alpha=0.05,level='genes',method="BH", useCuffMTC=FALSE)

Arguments

object	A CuffSet object (e.g. cuff)
x	Optional argument to restrict significance results to one pairwise comparison. Must be used with a 'y' argument to specificy the other half of the pair.
y	See x.
alpha	An alpha value by which to filter multiple-testing corrected q-values to determine significance
level	Feature level to be queried for significance (must be one of c('genes','isoforms','TSS','CDS')
method	Multiple testing method to be used for correction. (default: "BH")
useCuffMTC	Logical vector whether or not to use the multiple-testing corrected q-values from the cuffdiff analysis directly, or calculate new q-values from a subset of tests.

Details

This is a convenience function to quickly retrieve vectors of identifiers for genes or features that were determined to be significantly regulated between conditions by cuffdiff. This function only returns tracking IDs that correspond to tests with an 'OK' status from cuffdiff, NOTEST values are ignored. By default getSig returns a vector of IDs for all pairwise comparisons together. If you specify an 'x' AND 'y' values as sample names, then only the features that are significant in that particular pairwise comparison are reported, after appropriate multiple testing correction of output p-values.

Value

A vector of feature IDs.

Note

None.

Author(s)

Loyal A. Goff

References

None.

Examples

	a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data in sample directory and creates CuffSet object 'a'
	mySig<-getSig(a,x='hESC',y='Fibroblasts',alpha=0.05,level='genes')
	head(mySig)
	

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