R: Heritability estimation based on genomic relationship matrix...

h2.jags {gap} | R Documentation

## Heritability estimation based on genomic relationship matrix using JAGS

### Description

Heritability estimation based on genomic relationship matrix using JAGS

### Usage

    h2.jags(y,x,G,eps=0.0001,sigma.p=0,sigma.r=1,parms=c("b","p","r","h2"),...)

### Arguments

`y` | outcome vector
`x` | covariate matrix
`G` | genomic relationship matrix
`eps` | a positive diagonal perturbation to G
`sigma.p` | initial parameter values
`sigma.r` | initial parameter values
`parms` | monitored parmeters
`...` | parameters passed to jags, e.g., n.chains, n.burnin, n.iter

### Details

This function performs Bayesian heritability estimation using genomic relationship matrix.

### Value

The returned value is a fitted model from jags().

### References

Zhao JH, Luan JA, Congdon P (2018). Bayesian linear mixed models with polygenic effects. J Stat Soft 85(6):1-27

### Author(s)

Jing Hua Zhao

### Examples

    ## Not run:
    require(gap.datasets)
    set.seed(1234567)
    meyer <- within(meyer,{
        y[is.na(y)] <- rnorm(length(y[is.na(y)]),mean(y,na.rm=TRUE),sd(y,na.rm=TRUE))
        g1 <- ifelse(generation==1,1,0)
        g2 <- ifelse(generation==2,1,0)
        id <- animal
        animal <- ifelse(!is.na(animal),animal,0)
        dam <- ifelse(!is.na(dam),dam,0)
        sire <- ifelse(!is.na(sire),sire,0)
    })
    G <- kin.morgan(meyer)$kin.matrix*2
    library(regress)
    r <- regress(y~-1+g1+g2,~G,data=meyer)
    r
    with(r,h2G(sigma,sigma.cov))
    eps <- 0.001
    y <- with(meyer,y)
    x <- with(meyer,cbind(g1,g2))
    ex <- h2.jags(y,x,G,sigma.p=0.03,sigma.r=0.014)
    print(ex)

    ## End(Not run)

[Package gap version 1.2.3-1 Index]