BaderLab / EnrichmentMapApp

The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.
http://apps.cytoscape.org/apps/enrichmentmap
GNU Lesser General Public License v2.1
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enhancement RCy3: enrichmentmap build with Great: not able to filter using binomial q value (only hypergeometric test available) #494

Closed veroniquevoisin closed 1 year ago

veroniquevoisin commented 1 year ago

When we build an enrichmentmap from Great, we can filter the results based on the hypergeometric q value or the binomial test q value. When the map is being built, there is a pop up menu that gives us the choice between hypergeometric or binomial. However it is not possible with the current Rcy3 command. As a work around I'm thinking of building the map with qvalue of 1 and then filtering the nodes using the binomial qvalue by importing the original great result as node table.

mikekucera commented 1 year ago

Added a new argument called greatFilter to the enrichmentmap mastermap command.