topDSGenes {SeqGSEA} | R Documentation

## 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.

### Author(s)

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

### 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")

[Package SeqGSEA version 1.30.0 Index]