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Genemania through R #31

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valentinapapa opened this issue Dec 16, 2021 · 2 comments
Open

Genemania through R #31

valentinapapa opened this issue Dec 16, 2021 · 2 comments

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@valentinapapa
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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
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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 - GeneMANIA/genemania#170

@valentinapapa
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Thank you . When do you expect the next release?

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