enrichDO: DO Enrichment Analysis

Description Usage Arguments Value Author(s) See Also Examples

View source: R/enrichDO.R

Description

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

Usage

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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.

Author(s)

Guangchuang Yu http://guangchuangyu.github.io

See Also

enrichResult-class

Examples

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

DOSE documentation built on Nov. 8, 2020, 7:48 p.m.