Description Usage Arguments Examples
This function runs the BayesDiallel Gibbs Sampler for diallel cross data.
1 2 3 4 5 6 7 8 9 | diallel.gibbs(phenotype, sex = NULL, is.female = TRUE, mother.str,
father.str, n.iter = 1000, burn.in = 10000, multi.chain = 1,
thin = 1, sigma.2.starter = 5, tau_add.starter = 2,
tau_inbred.starter = 2, tau_mat.starter = 2,
tau_epi_sym.starter = 2, tau_epi_asym.starter = 2,
strains.reorder = c("AJ", "B6", "129", "NOD", "NZO", "CAST", "PWK",
"WSB"), strains.rename = c("AJ", "B6", "129", "NOD", "NZO", "CAST",
"PWK", "WSB"), use.constraint = TRUE, use.progress.bar = TRUE,
hyper.ga.alpha = 0.002, hyper.ga.beta = 2)
|
phenotype |
Vector of the phenotypes. Expects a quantitative phenotype. |
sex |
Binary vector for females and males. By default, expects females to be coded as 1 and males as 0. |
is.female |
DEFAULT: TRUE. If TRUE, then sex expects female=1 and male=0. If FALSE, then female=0 and male=1. |
mother.str |
Vector of strain identities of mother/dam. |
father.str |
Vector of strain identities of father/sire. |
n.iter |
DEFAULT: 1000. The number of samples to be collected. |
burn.in |
DEFAULT: 10000. The number of samples run as a burn-in, which are not stored. |
multi.chain |
DEFAULT: 1. The number of MCMC chains to run. |
thin |
DEFAULT: 1. If 1, no thinning is used. If 2, then every other sample is stored. If 3, then every third observation is stored. And so on. |
tau_add.starter |
DEFAULT: 2. Starting value for the variance parameter of the additive effects in the Gibbs Sampler. |
tau_inbred.starter |
DEFAULT: 2. Starting value for the variance parameter of the inbred effects in the Gibbs Sampler. |
tau_mat.starter |
DEFAULT: 2. Starting value for the variance parameter of the maternal effects in the Gibbs Sampler. |
tau_epi_sym.starter |
DEFAULT: 2. Starting value for the variance parameter of the symmetric epistatic effects in the Gibbs Sampler. |
tau_epi_asym.starter |
DEFAULT: 2. Starting value for the variance parameter of the asymmetric epistatic effects in the Gibbs Sampler. |
strains.reorder |
DEFAULT: c("AJ", "B6", "129", "NOD", "NZO", "CAST", "PWK", "WSB"). Orders the strains based on the standard ordering of Collaborative Cross founders |
strains.rename |
DEFAULT: c("AJ", "B6", "129", "NOD", "NZO", "CAST", "PWK", "WSB"). Renames the strains. By default, expects the founders of the Collaborative Cross. |
use.constraint |
DEFAULT: TRUE. Use a rotation matrix to reduce the dimension of strain matrices because the system is linearly dependent. Can result in narrower posterior intervals. |
use.progress.bar |
DEFAULT: TRUE. A progress bar shows how sampling is progressing. |
sigma2.starter |
DEFAULT: 5. Starting value for the residual error variance parameter in the Gibbs Sampler. |
1 |
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