KeggGeneSets: Create a list of KEGG gene sets

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 KEGG pathways terms. It is species-specific, and returns a list of gene sets, each of which is a character vector of Entrez gene identifiers.

Usage

KeggGeneSets(species = "Hs")

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").

Details

This function needs Internet connection and relies on the following packages: KEGGREST.

Value

A list of gene sets, with names as KEGG pathway IDs. Each gene set is a group of genes represented by Entrez identifiers.

See Also

GOGeneSets, MSigDBGeneSets

Examples

library(KEGGREST)
library(org.Hs.eg.db)
HS_KEGG <- KeggGeneSets(species = "Hs")

CityUHK-CompBio/HTSanalyzeR2 documentation built on Dec. 3, 2020, 2:35 a.m.