AtlasRDF (version 1.8.0)

getAllEnsemblGenesForExFactor: Get all ENSEMBL genes reported as differentially expressed for a given experimental factor.

Description

Get all ENSEMBL genes reported as differentially expressed for a given experimental factor. Returns the gene URI, ENSEMBL Id and common gene name.

Usage

getAllEnsemblGenesForExFactor(exfactor, limit, endpoint)

Arguments

exfactor

The URI of the experimental factor e.g. "efo:EFO_0001420"

limit

Limit the number of genes returned by the query to this, no limit specified or value of 0 returns all.

endpoint

SPARQL endpoint to query data from. Default value is the live Atlas SPARQL endpoint but this can be overidden.

Value

Data frame describing genes for the specified experimental factor with the following slots:

dbXref

the URI of the gene

geneName

the common name of the gene

ensemblid

the ENSEMBL id of the gene

propertyValue

the property value for this gene corresponding to the experimental factor in the query

Examples

###get the genes for the experimental factor 'sepsis' (efo:EFO_0001420)
#results <- getAllEnsemblGenesForExFactor("efo:EFO_0001420")
#results[1,] #first gene result