ReactomePA (version 1.12.3)

enrichPathway: Pathway Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enriched pathways with FDR control.

Description

Pathway Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enriched pathways with FDR control.

Usage

enrichPathway(gene, organism = "human", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.2, universe, minGSSize = 5, readable = FALSE)

Arguments

gene

a vector of entrez gene id.

organism

one of "human", "rat", "mouse", "celegans", "zebrafish", "fly".

pvalueCutoff

Cutoff value of pvalue.

pAdjustMethod

one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"

qvalueCutoff

Cutoff value of qvalue

universe

background genes

minGSSize

minimal size of genes annotated by Ontology term for testing.

readable

whether mapping gene ID to gene Name

Value

A enrichResult instance.

See Also

enrichResult-class

Examples

gene <- c("11171", "8243", "112464", "2194",
				"9318", "79026", "1654", "65003",
				"6240", "3476", "6238", "3836",
				"4176", "1017", "249")
	yy = enrichPathway(gene, pvalueCutoff=0.05)
	head(summary(yy))
	#plot(yy)