getGenesForExperimentURI: Get all of the genes reported in an experiment, speicifed by...

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

Description

Get all of the gene as reported within an experiment. The experiment is specified as an Atlas experiment URI e.g. <http://rdf.ebi.ac.uk/resource/atlas/E-GEOD-13396>

Usage

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

Arguments

experiment	Atlas experiment URI.
endpoint	The location of the SPARQL endpoint - default value is live Atlas endpoint

Value

data frame containg following elements

expressionValue	The summarised expression value for this gene
dbXref	The URI identifier for this gene
pvalue	The p-value representing differentially expression for this gene
propertyValue	The property value for which this gene was reported as differentially expressed

Author(s)

James Malone, Simon Jupp

Examples

###get genes for experiment <http://rdf.ebi.ac.uk/resource/atlas/E-GEOD-13396>
#Can take several minutes to complete
#res <- getGenesForExperimentURI("<http://rdf.ebi.ac.uk/resource/atlas/E-MEXP-3739>")
###list first gene in the experiment
#res[1,]

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