SeqGSEA (version 1.12.0)

topDSExons: Extract top differentially spliced exons

Description

This function is to extract top n differentially spliced exons, ranked by p-values or NB-stats.

Usage

topDSExons(RCS, n = 20, sortBy = c("pvalue", "NBstat"))

Arguments

RCS

a ReadCountSet object after running DSpermutePval.

n

the number of top genes.

sortBy

indicating whether p-value or NBstat to be used for ranking genes.

Value

A table for top n exons. Columns include: geneID, exonID, testable, NBstat, pvalue, padjust, and meanCounts.

See Also

topDSGenes, DSpermutePval

Examples

data(RCS_example, package="SeqGSEA")
permuteMat <- genpermuteMat(RCS_example, times=10)
RCS_example <- exonTestability(RCS_example)
RCS_example <- estiExonNBstat(RCS_example)
RCS_example <- estiGeneNBstat(RCS_example)
RCS_example <- DSpermutePval(RCS_example, permuteMat)
topDSExons(RCS_example, 10, "NB")