enrich.GSE {MAGeCKFlute}R Documentation

Gene set enrichment analysis

Description

A universal gene set enrichment analysis tools

Usage

enrich.GSE(geneList, keytype = "Symbol", type = "GOBP",
  organism = "hsa", pvalueCutoff = 0.25, limit = c(2, 200),
  gmtpath = NULL, nPerm = 2000, by = "fgsea", verbose = TRUE)

Arguments

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

Value

A enrichResult instance.

Author(s)

Wubing Zhang

See Also

enrich.HGT

enrich.ORT

EnrichAnalyzer

enrichResult-class

Examples

data(geneList, package = "DOSE")
## Not run: 
    enrichRes = enrich.GSE(geneList, keytype = "entrez")
    head(slot(enrichRes, "result"))

## End(Not run)


[Package MAGeCKFlute version 1.6.5 Index]