topDSExons {SeqGSEA} | R Documentation

## 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.

### Author(s)

Xi Wang, xi.wang@newcastle.edu.au

### 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")

[Package SeqGSEA version 1.24.0 Index]