enrich.GSE {MAGeCKFlute} | R Documentation |
A universal gene set enrichment analysis tools
enrich.GSE(geneList, keytype = "Entrez", type = "CORUM", organism = "hsa", pvalueCutoff = 0.25, pAdjustMethod = "BH", limit = c(3, 50), gmtpath = NA)
geneList |
A order ranked numeric vector with geneid as names. |
keytype |
"Entrez" or "Symbol". |
type |
Geneset category for testing, one of 'CORUM', 'CPX' (ComplexPortal), 'GOBP', 'GOMF', 'GOCC', 'KEGG', 'BIOCARTA', 'REACTOME', 'WikiPathways', 'EHMN', 'PID', or any combination of them (e.g. 'GOBP+GOMF+CORUM'), or 'All' (all categories). |
organism |
'hsa' or 'mmu'. |
pvalueCutoff |
Pvalue cutoff. |
pAdjustMethod |
One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". |
limit |
A two-length vector (default: c(3, 50)), specifying the minimal and maximal size of gene sets for enrichent analysis. |
gmtpath |
The path to customized gmt file. |
A enrichResult instance.
Wubing Zhang
data(geneList, package = "DOSE") ## Not run: enrichRes = enrich.GSE(geneList, type = "KEGG", organism="hsa") head(slot(enrichRes, "result")) ## End(Not run)