enrichPathway: Pathway Enrichment Analysis of a gene set. Given a vector of...

Description Usage Arguments Value Author(s) See Also Examples

View source: R/enrichPathway.R

Description

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

Usage

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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

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	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)

ReactomePA documentation built on Nov. 8, 2020, 5:40 p.m.