writeSigGeneSet {SeqGSEA} | R Documentation |
This function is to write the specified gene set (whose index is i) with significance information, including p-value and FDR, and gene scores for each gene in this set.
writeSigGeneSet(gene.set, i, gene.score, file = "")
gene.set |
an object of class SeqGeneSet with |
i |
the i-th gene set in the SeqGeneSet object. |
gene.score |
the vector of gene scores for running GSEA. |
file |
output file name, if not specified print to screen. |
See plotSigGeneSet
, which shows graphic information of the gene set specified.
Xi Wang, xi.wang@newcastle.edu.au
GSEnrichAnalyze
,
topGeneSets
,
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) topGeneSets(GS_example, n=5) writeSigGeneSet(GS_example, 9, gene.score) # 9th gene set is the most significant one.