search

hanchenphd / GMMAT

Generalized linear Mixed Model Association Tests
Other
36 stars 22 forks source link

SMMAT n.p==0 Error #56

Closed alexisregelson closed 1 year ago

alexisregelson commented 1 year ago

Hello,

I am running SMMAT and I keep getting this error, but I don't know what it means.

"Error in if (n.p == 0) next : missing value where TRUE/FALSE needed"

I first got it when I was looking at a subset of SNPs, so I included all SNPs on chromosome 1 and still got the error, so it seems unlikely that it's due to a small sample size.

Here is my code for reference:

model0 <- glmmkin(Base_AD ~ Sex, data = pheno, id = "SUBJID_SUBJID", family = binomial(link = "logit")) SMMAT(model0, group.file=genes, geno.file=gds, MAF.range=c(1e-7, 0.1), miss.cutoff=1, method="davies", tests="O")

Thank you, Alexis

alexisregelson commented 1 year ago

I believe I have figured out the issue.