GMMAT.R
In gaawr2: Genetic Association Analysis

run_GMMAT <- function()
{
  library(GMMAT)
  data(example,package="GMMAT")
  attach(example)
  model0 <- GMMAT::glmmkin(disease ~ age + sex, data = pheno, kins = GRM,
                           id = "id", family = binomial(link = "logit"))
  model1 <- GMMAT::glmmkin(fixed = trait ~ age + sex, data = pheno, kins = GRM,
                           id = "id", family = gaussian(link = "identity"))
  model2 <- GMMAT::glmmkin(fixed = trait ~ age + sex, data = pheno, kins = GRM,
                           id = "id", groups = "disease",
                           family = gaussian(link = "identity"))
  snps <- c("SNP10", "SNP25", "SNP1", "SNP0")
  geno.file <- system.file("extdata", "geno.bgen", package = "GMMAT")
  samplefile <- system.file("extdata", "geno.sample", package = "GMMAT")
  outfile <- "glmm.score.txt"
  GMMAT::glmm.score(model0, infile = geno.file, BGEN.samplefile = samplefile,
                    outfile = outfile)
  read.delim(outfile) |>
       head(n=4) |>
       knitr::kable(caption="Score tests under GLMM on four SNPs",digits=2)
  unlink(outfile)
  bed.file <- system.file("extdata", "geno.bed", package = "GMMAT") |>
              tools::file_path_sans_ext()
  model.wald <- GMMAT::glmm.wald(fixed = disease ~ age + sex, data = pheno,
                                 kins = GRM, id = "id", family = binomial(link = "logit"),
                                 infile = bed.file, snps = snps)
  knitr::kable(model.wald,caption="Wald tests under GLMM on four SNPs")
  detach(example)
}