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

In sunlightwang/SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

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, [e-mail]

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) 

sunlightwang/SeqGSEA documentation built on Dec. 5, 2020, 5:52 p.m.