Hi there,
When querying for variants that are in Open Targets in R, I noticed that some credible set variants have a posterior probability but do not have a L2G score; is this because “all [L2G] predictions below 0.05 are filtered out” with all of the data, or does the filtering only apply to the Platform website?
Hi @mjatoi,
All predictions below 0.05 are filtered out, from data, API and web.
The expectation is that if you didn’t find any L2G > 0.05, the model couldn’t produce even a vague prediction of the likely causal gene. There could be many reasons for that. For example, the causal gene could be beyond the cis-window under analysis or be a non-protein coding gene which are currently discarded. Future improvements in L2G will aim to improve our resolution on finding causal genes but at the moment we don’t have a reasonable prediction for such credible sets.
If strictly required, L2G < 0.05 can be recreated using gentropy and running the locus_to_gene.
I hope this helps 