myGWAS_fit: Fit a stan model.
In xulong82/bayes.glmm: A GWAS tool in Bayesian framework

Description Usage Arguments Value Author(s) See Also Examples

Fit a stan model.

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myGWAS_fit(model = "dummy", method = "dummy", type = "dummy",
  cov = NULL, geno = NULL, pheno = NULL, prior_non = 1, prior_inf = 0,
  iter = 1000, warmup = 200, chains = 3, cores = 3)

`model`	A stan model of rstan:stanmodel class.
`method`	Method to estimate model parameters ("optimizing", or "sampling").
`type`	Variable type of the response variable ("linear", "binary", "categorical").
`cov`	A matrix of model covariates.
`geno`	A vector of variant genotype data (0, 1, 2).
`pheno`	A vector of response variable data.

A list of model fit.

Xulong Wang, xwang@jax.org

rstan package which this function wraps

myGWAS_fit(mymodel, rebuild = F)
data("sample", package = "bayes.glmm")
pheno = data$pheno
geno = data$geno
cov = data$cov
L <- t(chol(data$K))
mymodel = stan_models(model = "glm")
y1 = myGWAS_fit(model = mymodel, method = "optimizing", type = "categorical", cov = cov, geno = geno[c(1, 3), ], pheno = pheno)
y2 = myGWAS_fit(model = mymodel, method = "sampling", type = "categorical", cov = cov, geno = geno[c(1, 3), ], pheno = pheno)