enrichment_analysis {MAGeCKFlute}R Documentation

Enrichment analysis

Description

Enrichment analysis

Usage

enrichment_analysis(geneList, universe = NULL, method = "ORT",
  type = "KEGG", organism = "hsa", pvalueCutoff = 0.25,
  qvalueCutoff = 0.2, pAdjustMethod = "BH", minGSSize = 2,
  maxGSSize = 50, plotTitle = NULL, color = "#3f90f7")

Arguments

geneList

A character vector or a ranked numeric vector(for GSEA) with names of geneid, specifying the genelist to do enrichment analysis.

universe

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

method

One of "ORT"(Over-Representing Test), "GSEA"(Gene Set Enrichment Analysis), "DAVID", "GOstats", and "HGT"(HyperGemetric test), or index from 1 to 5

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.

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.GOstats

enrich.DAVID

enrich.GSE

enrich.ORT

enrich.HGT

enrichResult-class

Examples

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


[Package MAGeCKFlute version 1.0.1 Index]