GSEnrichAnalyze {SeqGSEA} | R Documentation |
The main function of gene set enrichment analysis
GSEnrichAnalyze(gene.set, gene.score, gene.score.perm, weighted.type = 1)
gene.set |
a SeqGeneSet object. |
gene.score |
a vector of integrated gene scores in the same order as genes listed in the |
gene.score.perm |
a matrix of integrated gene scores on permutation data sets; row: genes; col: permutation. |
weighted.type |
weight type for gene scores; default: 1. |
A SeqGeneSet object with many slots updated, such as GSEA.ES
and GSEA.pval
.
Xi Wang, xi.wang@newcastle.edu.au
Xi Wang and Murray J. Cairns (2013). Gene Set Enrichment Analysis of RNA-Seq Data: Integrating Differential Expression and Splicing. BMC Bioinformatics, 14(Suppl 5):S16.
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, 5)