GOGeneSets: Create a list of gene sets based on Gene Ontology terms

Description Usage Arguments Details Value See Also Examples

View source: R/gsca_load_genesets.R

Description

This function creates a list of gene sets based on Gene Ontology terms. It is species-specific, and returns a list of gene sets, each of which is a character vector of Entrez identifiers.

Usage

1
GOGeneSets(species = "Hs", ontologies = c("MF"))

Arguments

species

A single character value specifying a choice of species, such as "Dm" ("Drosophila_melanogaster"), "Hs" ("Homo_sapiens"), "Rn" ("Rattus_norvegicus") or "Mm" ("Mus_musculus").

ontologies

A single character value or a character vector specifying an ontology or multiple ontologies. Valid format could be any combination of "BP", "MF" and "CC".

Details

This function relies on the following packages: AnnotationDbi, GO.db and the species db, such as org.Dm.eg.db.

Value

A list of gene sets, with names as GO IDs. Each gene set is a character vector of Entrez identifiers.

See Also

KeggGeneSets, MSigDBGeneSets

Examples

1
2
3
4
5
library(GO.db)
library(org.Hs.eg.db)
HS_GO_CC <- GOGeneSets(species="Hs",ontologies=c("CC"))

HS_GO <- GOGeneSets(species="Hs",ontologies=c("CC", "MF", "BP"))

CityUHK-CompBio/HTSanalyzeR2 documentation built on Dec. 11, 2018, 8:06 a.m.