AtlasRDF (version 1.8.0)

getRankedPathwaysForGeneIds: Get pathway names and URIs for given gene list, sorted into list with most common pathways first.

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

Examples

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