EnrichAnalyzer {MAGeCKFlute} | R Documentation

## Enrichment analysis

### Description

Enrichment analysis

### Usage

    EnrichAnalyzer(geneList, keytype = "Entrez", type = "CORUM+KEGG",
      method = "ORT", organism = "hsa", pvalueCutoff = 0.25,
      limit = c(1, 120), universe = NULL, filter = TRUE, 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).
`method` | One of "ORT"(Over-Representing Test), "GSEA"(Gene Set Enrichment Analysis), and "HGT"(HyperGemetric test).
`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.
`filter` | Boolean, specifying whether filter out redundancies from the enrichment results.
`gmtpath` | The path to customized gmt file.

### Value

`enrichRes` is an enrichResult instance.

### Author(s)

Wubing Zhang

### See Also

`enrich.GSE`

`enrich.ORT`

`enrich.HGT`

`enrichResult-class`

### Examples

    data(geneList, package = "DOSE")
    keggA = EnrichAnalyzer(geneList[1:500], method = "HGT")
    head(keggA@result)

[Package MAGeCKFlute version 1.4.3 Index]