Filter enrichment results to only include experimental factors of a given parent class (e.g. all cancers)

Share:

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

1
    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

1
2
3
4
    ###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)      

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.