enrich.GSE {MAGeCKFlute} | R Documentation |
A universal gene set enrichment analysis tools
enrich.GSE(geneList, type = "MsigDB_c2_h", organism = "hsa", minGSSize = 10, maxGSSize = 500, pvalueCutoff = 0.25, pAdjustMethod = "BH")
geneList |
A order ranked numeric vector with geneid as names. |
type |
A character, indicating geneset category for testing, "MsigDB_c2_h"(default). |
organism |
A character, specifying organism, only 'human' is available. |
minGSSize |
Minimal size of each geneSet for testing. |
maxGSSize |
Maximal size of each geneSet for analyzing. |
pvalueCutoff |
Pvalue cutoff. |
pAdjustMethod |
One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". |
A enrichResult instance.
Wubing Zhang
data(geneList, package = "DOSE") ## Not run: enrichRes = enrich.GSE(geneList, type = "KEGG", organism="hsa") head(enrichRes@result) ## End(Not run)