R: Mixed modeling with genetic relationship matrices

MCMCgrm {gap} | R Documentation

## Mixed modeling with genetic relationship matrices

### Description

Mixed modeling with genomic relationship matrix. This is appropriate with relationship matrix derived from family structures or unrelated individuals based on whole genome data.

### Usage

    MCMCgrm(
      model,
      prior,
      data,
      GRM,
      eps = 0,
      n.thin = 10,
      n.burnin = 3000,
      n.iter = 13000,
      ...
    )

### Arguments

`model` | statistical model.
`prior` | a list of priors for parameters in the model above.
`data` | a data.frame containing outcome and covariates.
`GRM` | a relationship matrix.
`eps` | a small number added to the diagonal of the a nonpositive definite GRM.
`n.thin` | thinning parameter in the MCMC.
`n.burnin` | the number of burn-in's.
`n.iter` | the number of iterations.
`...` | other options as appropriate for MCMCglmm.

### Details

The function was created to address a number of issues involving mixed modelling with family data or population sample with whole genome data. First, the implementaiton will shed light on the uncertainty involved with polygenic effect in that posterior distributions can be obtained. Second, while the model can be used with the MCMCglmm package there is often issues with the specification of pedigree structures but this is less of a problem with genetic relationship matrices. We can use established algorithms to generate kinship or genomic relationship matrix as input to the MCMCglmm function. Third, it is more intuitive to specify function arguments in line with other packages such as R2OpenBUGS, R2jags or glmmBUGS. In addition, our experiences of tuning the model would help to reset the input and default values.

### Value

The returned value is an object as generated by MCMCglmm.

### Author(s)

Jing Hua Zhao

### References

Hadfield JD (2010). MCMC Methods for multi-response generalized linear mixed models: The MCMCglmm R Package, J Stat Soft 33(2):1-22, https://www.jstatsoft.org/article/view/v033i02.

### Examples

    ## Not run:
    ### with kinship

    # library(kinship)
    # fam <- with(l51,makefamid(id,fid,mid))
    # s <-with(l51, makekinship(fam, id, fid, mid))
    # K <- as.matrix(s)*2

    ### with gap

    s <- kin.morgan(l51)
    K <- with(s,kin.matrix*2)
    prior <- list(R=list(V=1, nu=0.002), G=list(G1=list(V=1, nu=0.002)))
    m <- MCMCgrm(qt~1,prior,l51,K)
    save(m,file="l51.m")
    pdf("l51.pdf")
    plot(m)
    dev.off()

    # A real analysis on bats
    ## data
    bianfu.GRM <- read.table("bianfu.GRM.txt", header = TRUE)
    bianfu.GRM[1:5,1:6]
    Data <- read.table(file = "PHONE.txt", header = TRUE,
                       colClasses=c(rep("factor",3),rep("numeric",7)))
    ## MCMCgrm
    library("MCMCglmm")
    GRM <- as.matrix(bianfu.GRM[,-1])
    colnames(GRM) <- rownames(GRM) <- bianfu.GRM[,1]
    library(gap)
    names(Data)[1] <- "id"
    prior <- list(G = list(G1 = list(V = 1, nu = 0.002)), R = list(V = 1, nu = 0.002))
    model1.1 <- MCMCgrm(WEIGTHT ~ 1, prior, Data, GRM, n.burnin=100, n.iter=1000, verbose=FALSE)
    ## an alternative
    names(Data)[1] <- "animal"
    N <- nrow(Data)
    i <- rep(1:N, rep(N, N))
    j <- rep(1:N, N)
    s <- Matrix::spMatrix(N, N, i, j, as.vector(GRM))
    Ginv <- Matrix::solve(s)
    class(Ginv) <- "dgCMatrix"
    rownames(Ginv) <- Ginv@Dimnames[[1]] <- with(Data, animal)
    model1.2 <- MCMCglmm(WEIGTHT ~ 1, random= ~ animal, data = Data,
      ginverse=list(animal=Ginv), prior = prior, burnin=100, nitt=1000, verbose=FALSE)
    ## without missing data
    model1.3 <- MCMCglmm(Peak_Freq ~ WEIGTHT, random = ~ animal,
      data=subset(Data,!is.na(Peak_Freq)&!is.na(WEIGTHT)),
      ginverse=list(animal=Ginv), prior = prior, burnin=100, nitt=1000, verbose=FALSE)

    ## End(Not run)

[Package gap version 1.2.3-6 Index]