enrich.GSE {MAGeCKFlute}R Documentation

GSEA

Description

A universal gene set enrichment analysis tools

Usage

enrich.GSE(geneList, type = "MsigDB_c2_h", organism = "hsa",
  minGSSize = 10, maxGSSize = 500, pvalueCutoff = 0.25,
  pAdjustMethod = "BH")

Arguments

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".

Value

A enrichResult instance.

Author(s)

Wubing Zhang

See Also

enrich.HGT

enrich.DAVID

enrich.GOstats

enrich.ORT

enrichment_analysis

enrichResult-class

Examples

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

## End(Not run)


[Package MAGeCKFlute version 1.0.1 Index]