coloc.abf and check_dataset returen "missing value where TRUE/FALSE needed"

[huntPis]

hello, I am a beginner of coloc user, I got error when runing check_dataset and coloc.abf, my input list dose not have any NA, here is my code
##########################
#check input

anyNA(list1)
[1] FALSE
anyNA(list2)
[1] FALSE
str(list1)

str(list1)
List of 8
$ position: num [1:114593] 79797290 79788248 79896888 79552681 79552543 ...
$ pvalues : num [1:114593] 0.75524 0.671048 0.000152 0.937623 0.937038 ...
$ type : chr "quant"
$ N : num [1:114593] 35892 35892 35892 35892 35892 ...
$ MAF : num [1:114593] 0.0132 0.0132 0.0177 0.3483 0.3138 ...
$ snp : chr [1:114593] "rs74532386" "rs145328330" "rs200058464" "rs445605" ...
$ beta : num [1:114593] 0.011 0.0151 0.1183 -0.0006 0.0006 ...
$ varbeta : num [1:114593] 1.21e-04 2.28e-04 1.40e-02 3.60e-07 3.60e-07 ...

str(list2)
List of 8
$ position: num [1:114593] 80089632 80080590 80189230 77312681 77312543 ...
$ pvalues : num [1:114593] 5.19e-06 8.95e-06 4.68e-05 7.06e-05 8.60e-05 ...
$ type : chr "cc"
$ N : num [1:114593] 6165 6165 6165 6165 6165 ...
$ MAF : num [1:114593] 0.0218 0.0214 0.0222 0.3759 0.3433 ...
$ snp : chr [1:114593] "rs74532386" "rs145328330" "rs200058464" "rs445605" ...
$ beta : num [1:114593] -0.857 0.838 0.736 0.209 -0.206 ...
$ varbeta : num [1:114593] 0.7343 0.7014 0.5423 0.0437 0.0423 ...

##run coloc
check_dataset(list2,warn.minp=1e-10)
res0 <- coloc.abf(dataset1=list1, dataset2=list2, p1 = 1e-04, p2 = 1e-04, p12 = 1e-05)
##########################
I got same error "
Error in if (min(p) > warn.minp) warning("minimum p value is: ", format.pval(min(p)), :
missing value where TRUE/FALSE needed"

Thank you for your assistance.

[pottj]

Hello,
I ran into the same problem (two continuous traits, no NAs, but the same error message), and I fixed it by checking and filtering all SNPs with beta == 0 in my first trait (2 SNPs). I guess when approximating the sdY from beta, varbeta, N, and MAF, beta must not be 0?
Maybe this helps in your case as well?