getRankedPathwaysForGeneIds: Get pathway names and URIs for given gene list, sorted into...

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

Description

Given a list of ENSEMBL gene IDs, the function will find pathways which these genes are involved in. These pathways will be grouped and ranked according to those with highest number of genes in common.

Usage

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

Arguments

genelist	The list of ENSEMBL gene IDs to find pathways for.
endpoint	The location of the SPARQL endpoint - default value is live Atlas endpoint

Value

A ranked list (pathway with greatest number of genes first) of pathwayresult classes with the following slots:

pathwayuri	The URI of the corresponding pathway
label	The textual human readable name of the pathway
numgenes	A count of the number of genes from the gene list associated with this pathway
genes	Vector of genes from the gene list that are associated with this pathway

Author(s)

James Malone, Simon Jupp

Examples

    ##get pathways which have the phrase 'ligand binding' included in their name
    #genes <- c("ENSRNOG00000034254", "ENSRNOG00000009325", "ENSRNOG00000033065", "ENSRNOG00000015518", "ENSRNOG00000048955", "ENSRNOG00000031230")
    #pathwaylist <- getRankedPathwaysForGeneIds(genes)

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.