KEGG enrichment analysis

Usage

KEGGEnrichment(
  gene_list,
  Species = "Homo",
  genelist_idtype,
  pvalueCutoff = 0.05,
  qvalueCutoff = 0.2,
  minGSSize = 10,
  maxGSSize = 500
)

Arguments

gene_list: The list of genes, which is required to be ensembl_gene_id, external_gene_name, entrezgene_id one of the three gene types.
Species: Select the species, Homo or Mus.
genelist_idtype: There are ensembl_gene_id, external_gene_name, entrezgene_id types of genetic IDs to choose from.
pvalueCutoff: Cutoff value of pvalue.
qvalueCutoff: Cutoff value of qvalue.
minGSSize: Minimal size of genes annotated by Ontology term for testing.
maxGSSize: Maximal size of genes annotated for testing.

Value

A KEGG object.

Examples

library(linkage)
library(LinkageData)
Geneset <- system.file("extdata", "SASPGeneSet.rdata", package = "LinkageData")
load(Geneset)
KEGG <-
  KEGGEnrichment(
    gene_list = SASPGeneSet,
    Species = "Homo",
    genelist_idtype = "external_gene_name"
  )
#> Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
#> Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/hsa"...