KeggGeneSets: Create a list of gene sets based on KEGG pathways terms

In HTSanalyzeR: Gene set over-representation, enrichment and network analyses for high-throughput screens

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="Dm")

Arguments

species

a single character value specifying the species: "Dm" ("Drosophila_ melanogaster"), "Hs" ("Homo_sapiens"), "Rn" ("Rattus_norvegicus"), "Mm" ("Mus_musculus") or "Ce" ("Caenorhabditis_elegans"))

Details

This function relies on the following packages: GSEABase, KEGG.db.

Value

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

Author(s)

Camille Terfve, Xin Wang

See Also

GOGeneSets

Examples

library(org.Dm.eg.db)
library(KEGG.db)
DM_KEGG<-KeggGeneSets(species = "Dm")

HTSanalyzeR documentation built on Oct. 31, 2019, 7:10 a.m.