AtlasRDF (version 1.8.0)

excludeSubclasses: Exclude subclasses of factors from enrichment results

Description

Removes all factors which are subclasses of a specified type from Atlas gene set enrichment results. For instance, if all chemical compounds were to be excluded form the enrichment results or all subclasses of cancer use this function.

Usage

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

Arguments

filterparentclass

The class from which all subclasses will be excluded - including this class.

resultset

Result set from an Atlas gene set enrichment.

endpoint

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

Value

new enrichment result set with the specified class and subclasses excluded.

Examples

####filter out all subclasses of chemical compounds from the result set
#####enrichment results has been produced using the enrichment functions in AtlasRDF package
#filteredresults <- excludeSubclasses("obo:CHEBI_37577", enrichmentresults)
#vizPvalues(filteredresults, 0.01)