enrichment_analysis {MAGeCKFlute} | R Documentation

## Enrichment analysis

### Description

Enrichment analysis

### Usage

    enrichment_analysis(geneList, method = "HGT", keytype = "Entrez",
      type = "KEGG", organism = "hsa", pvalueCutoff = 0.25,
      pAdjustMethod = "BH", limit = c(3, 50), universe = NULL,
      plotTitle = NULL, color = "#3f90f7")

### Arguments

`geneList` | A numeric vector with gene as names.
`method` | One of "ORT"(Over-Representing Test), "GSEA"(Gene Set Enrichment Analysis), and "HGT"(HyperGemetric test).
`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.
`universe` | A character vector, specifying the backgound genelist, default is whole genome.
`plotTitle` | Same as 'title' in 'plot'.
`color` | Color of points.

### Value

A list, including two items, `gridPlot` and `enrichRes`. `gridPlot` is a ggplot object, and `enrichRes` is a enrichResult instance.

### Author(s)

Feizhen Wu

### See Also

`enrich.GSE`

`enrich.ORT`

`enrich.HGT`

`enrichResult-class`

### Examples

    data(geneList, package = "DOSE")
    genes <- geneList[1:100]
    keggA = enrichment_analysis(genes, method = "HGT", type = "KEGG")
    print(keggA$gridPlot)

[Package MAGeCKFlute version 1.2.3 Index]