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]