excludeSubclasses: Exclude subclasses of factors from enrichment results
In AtlasRDF: Gene Expression Atlas query and gene set enrichment package.

Description Usage Arguments Value Author(s) Examples

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.

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

`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.

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

James Malone, Simon Jupp

####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)

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