Han Chen

Hi Yu, Unfortunately it was a convergence issue in your dataset that we could not really help with as the software developer. The likelihood function was monotonous with respect to...

Hi LL, This is not the estimated heritability as you are using a logit link function. Best, Han

Unfortunately, it is unclear to me how to derive that based on the logit link function.

If your files are all located in the working directory, you should directly provide the file prefix to the `infile` argument. What you did above was trying to find a...

The function `glmm.wald` does not allow the `snps` argument to be `NULL`. Please see Section 5.2.2 of the [user manual](https://github.com/hanchenphd/GMMAT/blob/master/inst/doc/GMMAT.pdf) for an example.

No, it has to be a character vector. Please read the help document in R. Are you trying to run the Wald test genome-wide? I would strongly recommend that you...

Hi Grace, Thank you for your interest in SMMAT! I have not seen this issue before, but I guess the problem was probably because this tri-allelic marker was ordered differently...

Hi Andrew, Have you tried fixing the order in your group definition file (instead of the order in GDS) as I suggested above? If you could send me a small...

Can you turn on `verbose = TRUE` and see if there are any numerical or convergence issues?

The problem came from your 20 dummy variables for center. In a logistic model, a regression coefficient of 30 is equivalent to an odds ratio of exp(30) = 10^13, and...