getSpeciesSpecificEnsemblGenesForExFactor: Get ENSEMBL genes which have been differentially expressed...

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

Description

Get the ENSEMBL gene IDs and names which are reported as differentially expressed in Atlas for a specified conditions and species.

Usage

getSpeciesSpecificEnsemblGenesForExFactor(exfactor, taxon, limit = 0, endpoint="http://www.ebi.ac.uk/rdf/services/atlas/sparql")

Arguments

exfactor	URI of the experimental factor search term
taxon	URI of the species to limit search to
limit	Optional limit to number of genes returned (default is all)
endpoint	The location of the SPARQL endpoint - default value is live Atlas endpoint

Value

data frame of results with the following:

dbXref	URI identifier of the gene
genename	Common gene name
ensemblid	ENSEMBL ID of gene

Author(s)

James Malone, Simon Jupp

Examples

###get genes differentially expressed for HeLa cells (efo:EFO_0001185) in human (obo:NCBITaxon_9606)
#getSpeciesSpecificEnsemblGenesForExFactor("efo:EFO_0001185", "obo:NCBITaxon_9606")

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