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

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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

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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) 

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