GO enrichment analysis

GO enrichment analysis

Usage

GOEnrichment(
  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 GO object.

Examples

library(Linkage)
data("SASPGeneSet")
go <-
  GOEnrichment(gene_list = SASPGeneSet,
               Species = "Homo",
               genelist_idtype = "external_gene_name")