getAllEnsemblGenesForExFactor: Get all ENSEMBL genes reported as differentially expressed...
In AtlasRDF: Gene Expression Atlas query and gene set enrichment package.

Description Usage Arguments Value Author(s) Examples

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

1	getAllEnsemblGenesForExFactor(exfactor, limit, endpoint)

`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.

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

James Malone, Simon Jupp

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

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