SeqGSEA (version 1.12.0)

topDSGenes: Extract top differentially spliced genes

Description

This function to extract top n differentially spliced genes, ranked by p-values or NBstats.

Usage

topDSGenes(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 genes. Columns include: geneID, NBstat, pvalue, and padjust.

See Also

topDSExons, 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)
topDSGenes(RCS_example, 10, "NB")