In gkeele/Diploffect.INLA: INLA Implementation of the Diploffect Model

Diploffect.INLA

This package contains an importance sampling-based integrated nested Laplace approximation (INLA) implementation of the Diploffect model to estimate Bayesian posterior distributions of genetic effects while taking into account haplotype uncertainty.

Required (or useful) non-CRAN R packages

This package requires the INLA R package, which is not available through CRAN.

Data structures

In addition to phenotype values, the Diploffect package requires that each individual has a set of diplotype (founder haplotype pair identity) probabilities for the locus. These diplotype probabilities can be provided directly as a matrix, or, for backwards compatibility, they can be provided as a data directory as would be output from the haplotype reconstruction method HAPPY (Mott et al. 2000), henceforth described as a genome cache. If the diplotype probabilities are stored in a genome cache, Diploffect.INLA can make use of convenience utilities to run the Diploffect model.

Example

First, install the package from Github.

devtools::install_github("gkeele/Diploffect.INLA")

library(Diploffect.INLA)
data(exampleCC)
data(locusmatrix)

inla.diploffect <- run.diploffect.inla(formula=y~1+(1|strain)+(1|dose.date), add.on=FALSE,                     
                                       data=exampleCC, K=NULL, prob.matrix=locusmatrix,
                                       num.draws=10, use.dip.lincomb=TRUE, seed=1, 
                       gamma.rate=1, impute.on="CCline")