Colocalization Coloc - Error in if (min(p) > warn.minp)

Question

[J]

I have been getting the following error using the most recent version of coloc:

Error in if (min(p) > warn.minp) warning("minimum p value is: ", format.pval(min(p)), :
missing value where TRUE/FALSE needed

I have checked the datasets and have confirmed that there are no missing entries for p-values in my dataset, or any other variable for that matter. I got no such errors with other eQTL data that I was using. I am at a loss and could use any advice.

[ATpoint]

Cannot help with the tool but the error appears if inside an if condition you compare elements and one is NA, for example

if(1==NA) message("FOO")

Here that means either min(p) or warn.minp is NA. If this is on GitHub maybe try and open an issue, things like that should be detected up front before such an error comes up I guess.

[bobmcpop]

I'm having the same problem. Did you find an answer?

[msoliai20]

I'm running into the same exact problem as well. Did you happen to find a solution? Thanks.

Answer 1

[Maristella]

I had the same problem, I solved excluding betas =0 or NA.