EnrichAnalyzer {MAGeCKFlute} | R Documentation

## Enrichment analysis

### Description

Enrichment analysis

### Usage

    EnrichAnalyzer(
      geneList,
      keytype = "Symbol",
      type = "Pathway+GOBP",
      method = "HGT",
      organism = "hsa",
      pvalueCutoff = 0.25,
      limit = c(2, 200),
      universe = NULL,
      filter = FALSE,
      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').
`method` | One of "ORT"(Over-Representing Test), "GSEA"(Gene Set Enrichment Analysis), and "HGT"(HyperGemetric test).
`organism` | 'hsa' or 'mmu'.
`pvalueCutoff` | FDR cutoff.
`limit` | A two-length vector (default: c(2, 200)), 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.
`verbose` | Boolean

### 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")
    ## Not run:
      keggA = EnrichAnalyzer(geneList[1:500], keytype = "entrez")
      head(keggA@result)

    ## End(Not run)

[Package MAGeCKFlute version 1.12.0 Index]