enrich.GSE {MAGeCKFlute}R Documentation

GSEA

Description

A universal gene set enrichment analysis tools

Usage

enrich.GSE(geneList, keytype = "Entrez", type = "CORUM",
  organism = "hsa", pvalueCutoff = 0.25, pAdjustMethod = "BH",
  limit = c(3, 50), gmtpath = NA)

Arguments

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.

Value

A enrichResult instance.

Author(s)

Wubing Zhang

See Also

enrich.HGT

enrich.ORT

enrichment_analysis

enrichResult-class

Examples

data(geneList, package = "DOSE")
## Not run: 
    enrichRes = enrich.GSE(geneList, type = "KEGG", organism="hsa")
    head(slot(enrichRes, "result"))

## End(Not run)


[Package MAGeCKFlute version 1.2.3 Index]