Filter enrichment results to only include experimental factors of a given parent class (e.g. all cancers)
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.
includeOnlySubclasses(includeparentclass, resultset, endpoint = "http://www.ebi.ac.uk/rdf/services/atlas/sparql")
The URI of the parent class for which all experimental factor subclasses will be included (removing all others).
The full enrichment result set
The location of the SPARQL endpoint - default value is live Atlas endpoint
New Atlas enrichment result set, filtered to include only experimental factors specified in the function call.
James Malone, Simon Jupp
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###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)