getSigTable: getSigTable

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 test table - like format.

Usage

## S4 method for signature 'CuffSet'
getSigTable(object,alpha=0.05,level='genes')

Arguments

object	A CuffSet object (e.g. cuff)
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')

Details

This is a convenience function to quickly retrieve lists 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 or reported as NA. By default getSig returns a table of genes x conditions, where the column names represent the pairwise comparisons from the cuffdiff analysis. The values in the table are 1 for features that are significant for this comparison and 0 for genes that are not, any failed tests are reported as <NA>.Only includes the features that are significant in at least one comparison.

Value

A data.frame of pairwise test results.

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'
	mySigTable<-getSigTable(a,alpha=0.05,level='genes')
	head(mySigTable)
	

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