getKEGGdata {domainsignatures}R Documentation

Fetch KEGG annotations and InterPro domains

Description

Get all available KEGG annotations and InterPro domains for a set of entrezgene identifiers from the KEGG annotation package and from the ensembl biomaRt.

Usage

getKEGGdata(universe, pathways)

Arguments

universe Character vector of entrezgene identifiers. This is the global universe of genes to test against.
pathways Optional character vector of KEGG pathway identifiers. This can be used in order to test for over-representation of only a subset of all the available KEGG pathways.

Details

This function is a wrapper around the KEGG annotation package and a customized query of the ensembl biomaRt database. For the gene identifiers in universe and all KEGG pathways it will fetch the necessary information and create an object of class ipDataSource which can later be used as input to gseDomain

Value

An object of class ipDataSource.

Author(s)

Florian Hahne

See Also

gseDomain

Examples

getKEGGdata()

[Package domainsignatures version 1.2.0 Index]