getGeneSets: Get gene sets

In RCPA: Consensus Pathway Analysis

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)

RCPA documentation built on Nov. 21, 2023, 5:08 p.m.