enrichPathway {ReactomePA}

R Documentation

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 = 10,
  maxGSSize = 500,
  readable = FALSE
)

Arguments

gene	a vector of entrez gene id.
organism	one of "human", "rat", "mouse", "celegans", "yeast", "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.
maxGSSize	maximal size of each geneSet for analyzing
readable	whether mapping gene ID to gene Name

Value

A enrichResult instance.

Author(s)

Guangchuang Yu http://ygc.name

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)

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