Filling of is_directed, is_stimulation, is_inhibition in cellchat_pipe.r

[wjjnnn]

Hi! Thank you for developing such a useful tool. Here, I have a question to consult. I noticed that the cellchat_formatDB function in cellchat_pipe.r can convert prior information into a format that meets cellchat input requirements. In this function, if the original data does not include is_directed, is_stimulation, is_inhibition and other items, it will be supplemented and the value will be filled as 1. I would like to ask what is the basis for such filling. Thank you for your help.

[dbdimitrov]

Hi @wjjnnn,

Thank you for running liana and apologies for the delayed response.

This is largely used as a placeholder for resource which do not contain any information regarding the sign of interactions. That being said, running CellChat with an external resource (non-default) would typically mean that information such as pathways or cofactor is omitted.

Hope this helps!