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saezlab / CollecTRI

Gene regulatory network containing signed transcription factor-target gene interactions
GNU General Public License v3.0
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Error in collectri example #10

Closed pietrisko closed 1 year ago

pietrisko commented 1 year ago

Hello,

'organism' in collectri function does not accept strings, just numbers, as 9606L for human.

OmnipathR::collectri(organism='human', genesymbols=TRUE, loops=TRUE)

Also, what does it do 'loops' parameter? Thanks.

PauBadiaM commented 1 year ago

Hi @pietrisko,

Indeed, the raw function from OmnipathR does not accept strings, for that, please use the wrapper provided by decoupleR: decoupleR::get_collectri. Keep in mind that this function also deals with the AP1 and NFKB TF complexes which the one in OmnipathR does not. The loops parameter means that when building the network, loops are allowed (an edge that connects a node to itself), so that a TF can be the target of itself. Hope this is helpful!

smuellerd commented 1 year ago

Thanks for pointing this out @pietrisko! I corrected this in the example now.