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GeneMANIA data processing pipeline
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Genemania through R #31

Open valentinapapa opened 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?

risserlin commented 2 years ago

Unfortunately it doesn't look like the attributes are searchable in the current genemania command.

I have submitted a ticket so that hopefully gets added on the next release - https://github.com/GeneMANIA/genemania/issues/170

valentinapapa commented 2 years ago

Thank you . When do you expect the next release?