DOSE (version 2.10.6)

enrichDO: DO Enrichment Analysis

Description

Given a vector of genes, this function will return the enrichment DO categories with FDR control.

Usage

enrichDO(gene, ont = "DO", pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, minGSSize = 10, maxGSSize = 500, qvalueCutoff = 0.2, readable = FALSE)

Arguments

gene

a vector of entrez gene id

ont

one of DO or DOLite.

pvalueCutoff

pvalue cutoff

pAdjustMethod

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

universe

background genes

minGSSize

minimal size of genes annotated by NCG category for testing

maxGSSize

maximal size of each geneSet for analyzing

qvalueCutoff

qvalue cutoff

readable

whether mapping gene ID to gene Name

Value

A enrichResult instance.

See Also

enrichResult-class

Examples

data(geneList)
	gene = names(geneList)[geneList > 1]
	yy = enrichDO(gene, pvalueCutoff=0.05)
	summary(yy)