Is claudia.R the main code for coloc.abf?

[jielab]

Dear Chris:

Can you please quickly confirm that https://github.com/chr1swallace/coloc/blob/main/R/**claudia.R** is still the main code for the classsic method as described in your 2014 paper?

The end of that code is the credible.sets() function. But it is NOT used by the coloc.abf() function. So, I guess that I could ignore it when testing colocalization (not fine-mapping).

I stilll have difficulty to understand how checking the shape (configuration) of two regional plots shown as below could determine whether there is a single causal variant.

For the 8 SNPs shown in the plot, imagine that all the 5 blue SNPs have a positive association with the biomaker. But only 2 of these SNPs have a positive association with eQTL (while the other 3 SNPs have a negative association). Would the coloc.abs result be the same as if all the 5 SNPs also had a positive association with eQTL?

Best regards,
Jie