getGeneSets {RCPA}

Get gene sets

Description

This function retrieves gene sets for a given organism.

Usage

getGeneSets(
  database = c("KEGG", "GO"),
  org = "hsa",
  taxid = 9606,
  namespace = c("biological_process", "molecular_function", "cellular_component"),
  minSize = 1,
  maxSize = 1000,
  useCache = FALSE
)

Arguments

database

The database of the gene sets. E.g, KEGG, GO.

org

The organism abbreviation. E.g, hsa, mmu, dme, etc. To see the full list of supported organisms, visit https://www.genome.jp/kegg/catalog/org_list.html. This parameter is only used when database is KEGG.

taxid

The NCBI taxonomy ID of the organism. This parameter is only used when database is GO.

namespace

The namespace of the GO terms. E.g, biological_process, molecular_function, cellular_component.

minSize

The minimum size of the gene sets.

maxSize

The maximum size of the gene sets.

useCache

A boolean parameter specifying if using pre-saved downloaded geneset database. It is FALSE by default.

Value

A named list with three elements: database, genesets and names.

Examples

library(RCPA)

KEGGgenesets <- getGeneSets("KEGG", org = "hsa", 
                              minSize = 10, maxSize = 1000, useCache = TRUE)

GOterms <- getGeneSets("GO", taxid = 9606, 
                        namespace = "biological_process", 
                        minSize = 10, maxSize = 1000, useCache = TRUE)