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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.

Author(s)

See Also

Examples

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

Disease Ontology Semantic and Enrichment analysis

v3.16.0
Artistic-2.0
Authors
Guangchuang Yu [aut, cre], Li-Gen Wang [ctb], Vladislav Petyuk [ctb], Giovanni Dall'Olio [ctb], Erqiang Hu [ctb]
Initial release

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