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

In CityUHK-CompBio/HTSanalyzeR2: HTSanalyzeR2: An R package for functional annotation, network analysis and time series analysis of high-throughput data

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

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

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. 3, 2020, 2:35 a.m.