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]