I was wondering if there is a way to filter the NicheNet-v2 LR network to remove ligand-receptor pairs inferred through PPI databases.
In my analyses, I have noticed that some of the top predicted interactions comprise a few spurious ligand-receptor pairs (for example, CSF1-CSF3R), and as a result I have been looking for ways to filter the LR network to remove low-confidence LR pairs. In previous versions of the package, there used to be an option to filter to 'bonafide' ligand-receptor pairs by removing pairs annotated with the 'ppi_prediction' and 'ppi_prediction_go' values in the 'database' column of the ligand-receptor network - but as far as I can see, this functionality has been removed since the upgrade of the ligand-receptor database + prior model in nichenet V2.
Whilst it's possible to manually remove problematic LR pairs one by one, I was wondering if there was a more systematic approach I could take. I have tried following the script/functions used to generate the NicheNet-v2 LR network (provided on this zenodo page), but I have been unable to find a way to identify LR pairs inferred through PPI resources using the tools provided by omnipath (although I'm not very experienced with omnipath so maybe I'm missing something obvious).
Hi,
Thanks for providing such a useful tool!
I was wondering if there is a way to filter the NicheNet-v2 LR network to remove ligand-receptor pairs inferred through PPI databases.
In my analyses, I have noticed that some of the top predicted interactions comprise a few spurious ligand-receptor pairs (for example, CSF1-CSF3R), and as a result I have been looking for ways to filter the LR network to remove low-confidence LR pairs. In previous versions of the package, there used to be an option to filter to 'bonafide' ligand-receptor pairs by removing pairs annotated with the 'ppi_prediction' and 'ppi_prediction_go' values in the 'database' column of the ligand-receptor network - but as far as I can see, this functionality has been removed since the upgrade of the ligand-receptor database + prior model in nichenet V2.
Whilst it's possible to manually remove problematic LR pairs one by one, I was wondering if there was a more systematic approach I could take. I have tried following the script/functions used to generate the NicheNet-v2 LR network (provided on this zenodo page), but I have been unable to find a way to identify LR pairs inferred through PPI resources using the tools provided by omnipath (although I'm not very experienced with omnipath so maybe I'm missing something obvious).
Thanks! Alex