enrich.ORT {MAGeCKFlute} | R Documentation

## Do enrichment analysis using over-representation test

### Description

Do enrichment analysis using over-representation test

### Usage

    enrich.ORT(geneList, keytype = "Entrez", type = "CORUM+KEGG",
      organism = "hsa", pvalueCutoff = 0.05, limit = c(1, 120),
      universe = NULL, gmtpath = NA)

### Arguments

`geneList` | A numeric vector with gene 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.
`limit` | A two-length vector (default: c(1, 120)), specifying the minimal and maximal size of gene sets for enrichent analysis.
`universe` | A character vector, specifying the backgound genelist, default is whole genome.
`gmtpath` | The path to customized gmt file.

### Value

A enrichedResult instance.

### Author(s)

Wubing Zhang

### See Also

`enrich.HGT`

`enrich.GSE`

`EnrichAnalyzer`

`enrichResult-class`

### Examples

    data(geneList, package = "DOSE")
    genes <- geneList[1:100]
    enrichedRes <- enrich.ORT(genes)
    head(slot(enrichedRes, "result"))

[Package MAGeCKFlute version 1.4.3 Index]