dataSource: Contructor for annotation object

In domainsignatures: Geneset enrichment based on InterPro domain signatures

Description

This function creates the necessary annotation object of class ipDataSource containing the pathway and InterPro ID mappings.

Usage

dataSource(mapping, type = "generic")

Arguments

mapping	A named list providing a mapping between enterzgene identifiers and arbitrary groupings of genes or pathways.
type	The type of pathway. A character skalar.

Details

For genes without pathway membership, NA list items need to be included in mapping. The names of the list comprise the gene universe to test against. The function will access the ensembl biomaRt database in order to retrieve the necessary InterPro domain information.

Value

Object of class ipDataSource

Author(s)

Florian Hahne

See Also

gseDomain, getKEGGdata

Examples

if(interactive())
{
grouping <- list("653361"=c("pw1", "pw2"), "729230"="pw1",
                 "415117"="pw3") 
dataSource(grouping)
}

domainsignatures documentation built on May 2, 2018, 4:17 a.m.