enrich.GSE {MAGeCKFlute} | R Documentation |
A universal gene set enrichment analysis tools
enrich.GSE(geneList, keytype = "Symbol", type = "GOBP", organism = "hsa", pvalueCutoff = 0.25, limit = c(2, 200), gmtpath = NULL, nPerm = 2000, by = "fgsea", verbose = TRUE)
geneList |
A order ranked numeric vector with geneid as names. |
keytype |
"Entrez" or "Symbol". |
type |
Molecular signatures for testing, available datasets include Pathway (KEGG, REACTOME, C2_CP), GO (GOBP, GOCC, GOMF), MSIGDB (C1, C2 (C2_CP (C2_CP_PID, C2_CP_BIOCARTA), C2_CGP), C3 (C3_MIR, C3_TFT), C4, C6, C7, HALLMARK) and Complex (CORUM). Any combination of them are also accessible (e.g. 'GOBP+GOMF+KEGG+REACTOME'). |
organism |
'hsa' or 'mmu'. |
pvalueCutoff |
Pvalue cutoff. |
limit |
A two-length vector, specifying the minimal and maximal size of gene sets for enrichent analysis. |
gmtpath |
The path to customized gmt file. |
nPerm |
The number of permutations. |
by |
One of 'fgsea' or 'DOSE' |
verbose |
Boolean |
A enrichResult instance.
Wubing Zhang
data(geneList, package = "DOSE") ## Not run: enrichRes = enrich.GSE(geneList, keytype = "entrez") head(slot(enrichRes, "result")) ## End(Not run)