getGenesForPathwayURI: Get genes associated with a signalling pathway from Reactome.

In AtlasRDF: Gene Expression Atlas query and gene set enrichment package.

Description

Get genes that are associated with proteins which are in turn associated to a specific signalling pathway in Reactome.

Usage

getGenesForPathwayURI(pathwayuri, endpoint = "http://www.ebi.ac.uk/rdf/services/atlas/sparql")

Arguments

pathwayuri	The URI of a reactome pathway.
endpoint	SPARQL endpoint to query data from. Default value is the live Atlas SPARQL endpoint but this can be overidden.

Value

List of gene URIs for the pathway

Author(s)

James Malone, Simon Jupp

Examples

###get gene list for the pathway AKT Signaling in Cancer
#getGenesForPathwayURI("<http://identifiers.org/reactome/REACT_147727.2>")

Example output

Loading required package: hash
hash-3.0.1 provided by Decision Patterns

Loading required package: SPARQL
Loading required package: XML
Loading required package: RCurl
Loading required package: bitops

AtlasRDF documentation built on Nov. 17, 2017, 9:33 a.m.