includeOnlySubclasses: Filter enrichment results to only include experimental...

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

Description

Function which allows filtering of enrichment results to remove experimental factors apart from those factors which are a subclasses of a given parent class. For instance, include only disease factors or only cell types.

Usage

    includeOnlySubclasses(includeparentclass, resultset, endpoint = "http://www.ebi.ac.uk/rdf/services/atlas/sparql")

Arguments

includeparentclass	The URI of the parent class for which all experimental factor subclasses will be included (removing all others).
resultset	The full enrichment result set
endpoint	The location of the SPARQL endpoint - default value is live Atlas endpoint

Value

New Atlas enrichment result set, filtered to include only experimental factors specified in the function call.

Author(s)

James Malone, Simon Jupp

Examples

    ###include only experimental factors which are diseases in the enrichment results
    #filteredgenes <- includeOnlySubclasses("efo:EFO_0000408", mouseresults, endpoint="http://wwwdev.ebi.ac.uk/rdf/services/atlas/sparql")
    ###view results
    #vizPvalues(filteredgenes)      

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