enrichKEGG2: KEGG Pathway Enrichment with Hypergeometric Test

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

KEGG Pathway Enrichment with Hypergeometric Test

Description

Given a vector of gene identifiers, this function returns KEGG pathway enrichment results based on a hypergeometric test with duplication support in the test set.

Usage

enrichKEGG2(
  gene,
  organism = "hsa",
  keyType = "kegg",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  minGSSize = 5,
  maxGSSize = 500,
  qvalueCutoff = 0.2,
  readable = FALSE
)

Arguments

gene	a vector of entrez gene ids (here the test set)
organism	supported organism are listed in http://www.genome.jp/kegg/catalog/org_list.html
keyType	one of "kegg", 'ncbi-geneid', 'ncbi-proteinid' or 'uniprot'
pvalueCutoff	pvalue cutoff
pAdjustMethod	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
universe	background genes
minGSSize	minimal size of genes annotated by ontology term for testing.
maxGSSize	maximal size of genes annotated for testing
qvalueCutoff	qvalue cutoff
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.

Examples

# Method supports duplicated elements in "gene", which should be entrez ids
gene <- c(rep("4312",4), rep("8318",2), "991", "10874")
#data(geneList, package="DOSE")
#kk <- enrichKEGG2(gene = gene, universe=names(geneList))
#head(kk)

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