enrichReactome: Reactome Enrichment Analysis of a gene set. Given a vector of...

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enrichReactomeR Documentation

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

Description

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

Usage

enrichReactome(
  gene,
  organism = "human",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  qvalueCutoff = 0.2,
  universe,
  minGSSize = 5,
  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 functional term for testing.

maxGSSize

maximal size of each gene set for analyzing

readable

TRUE or FALSE indicating whether to convert gene Entrez ids to gene Symbols in the 'itemID' column in the FEA result table.

Value

A feaResult instance.

See Also

feaResult-class

Examples

# This method supports duplicated elements in "gene"
gene <- c(rep("4312",4), rep("8318",2), "991", "10874")
#data(geneList, package="DOSE")
#rc <- enrichReactome(gene=gene, universe=names(geneList))
#result(rc)

yduan004/signatureSearch documentation built on Feb. 19, 2024, 9:30 a.m.