Error in GMMAT

[zhangyuan5422]

I can succesfully run the glmm.score model, but when i run the SMMAT command, it output partial results and reported the error: Error in if (n.p == 0) next : missing value where TRUE/FALSE needed Calls: SMMAT Execution halted my command look like this, does it something wrong:

out <- SMMAT(model0, group.file = group.file, geno.file = geno.file, MAF.range = c(1e-7, 0.5), miss.cutoff = 1, method = "davies", tests = c("O","E"),meta.file.prefix = "SMMAT.meta") 

write.csv(out, file = "SMMAT_output.csv", row.names = FALSE)

Would you please give me some suggestions? thanks.

[hanchenphd]

I would be happy to take a look if you could send me a reproducible example.

Thanks, Han

[zhangyuan5422]

Dear Han,

I have find the problem that the ref allel look like this (e.g., GACGACAGCGCTTTCATGGAGCCGAGGT) report the error: Error in if (n.p == 0) next : missing value where TRUE/FALSE needed.

I also have another question, whether GMMAT is right to run the family-based rare variants analysis, my genetic data based on famliy members (patient, his father, mother, and sibling).

Thanks Yuan

[hanchenphd]

Hi Yuan,

Yes, generalized linear mixed models as implemented in GMMAT have been applied to family data.

Best, Han