mixed | R Documentation |
Solve linear mixed model using restricted maximum likelihood (REML). Multiple variance components can be estimated.
mixed(fix = NULL, y, kk)
fix |
a design matrix of the fixed effects. If not passed, a vector of ones is added for the intercept. |
y |
a vector of the phenotypic values. |
kk |
a list of one or multiple kinship matrices. |
A list with following information is returned:
$v_i the inverse of the phenotypic variance-covariance matrix
$var estimated variance components of genetic effects
$ve estimated residual variance
$beta estimated fixed effects
Xu S, Zhu D and Zhang Q. (2014) Predicting hybrid performance in rice using genomic best linear unbiased prediction. Proc. Natl. Acad. Sci. USA 111, 12456-12461.
## load example data from hypred package data(hybrid_phe) data(input_geno) ## convert original genotype inbred_gen <- convertgen(input_geno, type = "hmp2") ## infer the additive and dominance genotypes of hybrids gena <- infergen(inbred_gen, hybrid_phe)$add gend <- infergen(inbred_gen, hybrid_phe)$dom ## calculate the additive and dominance kinship matrix ka <- kin(gena) kd <- kin(gend) ## for the additive model parm <- mixed(y = hybrid_phe[,3], kk = list(ka)) ## for the additive-dominance model parm <- mixed(y = hybrid_phe[,3], kk = list(ka, kd))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.