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cytoscape / RCy3

New version of RCy3, redesigned and collaboratively maintained by Cytoscape developer community
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GeneMania Attributes #165

Closed valentinapapa closed 2 years ago

valentinapapa commented 2 years ago

Hello, I'm trying to use genemania through R. The problem I encounter is in importing some types of networks. I would need to create a network with the following characteristics: organism = Homo Sapiens networks = Pathway, Genetic Interactions, Physical Interactions, Predicted, Consolidated-Pathways-2013 combiningMethod = Go biological process-based attrLimit = 100 geneLimit = 100 genes = KRAS

For this reason, the query I enter is:

genemania_command<- "genemania search organism=9606 networks=path,pi,gi,predict combiningMethod=BP attrLimit=100 geneLimit=100 genes= KRAS" commandsRun(genemania_command)

How can I also provide the Consolidated-Pathways-2013 as input? Furthermore, for another type of network, I would need to provide the Drug-interactions-2020 attribute as input. How can I do?

AlexanderPico commented 2 years ago

Sorry for the delayed response. This is not an RCy3 issue, however. The GeneMANIA app developers are responsible for defining the supported commands and attributes for their app. RCy3 simply passes them along to CyREST.

If you have a query that works in CyREST or in the Command Line Tool in Cytoscape, but not in RCy3, then we'd have an RCy3 bug.