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 = "Symbol",
      type = "GOBP",
      organism = "hsa",
      pvalueCutoff = 0.25,
      limit = c(2, 200),
      universe = NULL,
      gmtpath = NULL,
      verbose = TRUE
    )

### Arguments

`geneList` | A numeric vector with gene 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.
`universe` | A character vector, specifying the backgound genelist, default is whole genome.
`gmtpath` | The path to customized gmt file.
`verbose` | Boolean

### 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, keytype = "entrez")
    head(slot(enrichedRes, "result"))

[Package MAGeCKFlute version 1.7.2 Index]