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

In girke-lab/signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

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)

girke-lab/signatureSearch documentation built on Feb. 21, 2024, 8:32 a.m.