plotSig {SeqGSEA} | R Documentation

## Plot showing SeqGeneSet's p-values/FDRs vs. NESs

### Description

The function is to generate a plot of p-values (FDRs) versus normalized enrichment scores (NES). It also shows the distribution of p-values (FDRs) in this gene set category.

### Usage

    plotSig(gene.set, pdf = NULL)

### Arguments

`gene.set` | a SeqGeneSet object after running `GSEnrichAnalyze`.
`pdf` | whether to save the plot to PDF file; if yes, provide the name of the PDF file.

### Author(s)

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

### See Also

`GSEnrichAnalyze`, `plotSigGeneSet`

### Examples

    data(DEscore, package="SeqGSEA")
    data(DSscore, package="SeqGSEA")
    gene.score <- geneScore(DEscore, DSscore, method="linear", DEweight = 0.3)
    data(DEscore.perm, package="SeqGSEA")
    data(DSscore.perm, package="SeqGSEA")
    gene.score.perm <- genePermuteScore(DEscore.perm, DSscore.perm, method="linear",  DEweight=0.3)
    data(GS_example, package="SeqGSEA")
    GS_example <- GSEnrichAnalyze(GS_example, gene.score, gene.score.perm)
    plotSig(GS_example)

[Package SeqGSEA version 1.30.0 Index]