enrichKEGG2: KEGG Pathway Enrichment with Hypergeometric Test

View source: R/oraAnalyzer.R

enrichKEGG2R Documentation

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.