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hanchenphd / GMMAT

Generalized linear Mixed Model Association Tests
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Error in GMMAT #57

Open zhangyuan5422 opened 10 months ago

zhangyuan5422 commented 10 months ago

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 commented 10 months ago

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

Thanks, Han

zhangyuan5422 commented 10 months ago

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 commented 10 months ago

Hi Yuan,

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

Best, Han