plotSig {SeqGSEA} | R Documentation |
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.
plotSig(gene.set, pdf = NULL)
gene.set |
a SeqGeneSet object after running |
pdf |
whether to save the plot to PDF file; if yes, provide the name of the PDF file. |
Xi Wang, xi.wang@newcastle.edu.au
GSEnrichAnalyze
,
plotSigGeneSet
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)