enrich.ORT {MAGeCKFlute}R Documentation

Do enrichment analysis using over-representation test

Description

Do enrichment analysis using over-representation test

Usage

enrich.ORT(gene, universe = NULL, type = "KEGG", organism = "hsa",
  pvalueCutoff = 0.25, qvalueCutoff = 0.2, pAdjustMethod = "BH",
  minGSSize = 2, maxGSSize = 50)

Arguments

gene

A character vector, specifying the genelist to do enrichment analysis.

universe

A character vector, specifying the backgound genelist, default is whole genome.

type

Geneset category for testing, KEGG(default).

organism

A character, specifying organism, such as "hsa" or "Human"(default), and "mmu" or "Mouse"

pvalueCutoff

Pvalue cutoff.

qvalueCutoff

Qvalue cutoff.

pAdjustMethod

One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".

minGSSize

Minimal size of each geneSet for testing.

maxGSSize

Maximal size of each geneSet for analyzing.

Value

A enrichResult instance.

Author(s)

Wubing Zhang

See Also

enrich.HGT

enrich.DAVID

enrich.GOstats

enrich.GSE

enrichment_analysis

enrichResult-class

Examples

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


[Package MAGeCKFlute version 1.0.1 Index]