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.

This package requires the INLA R package,
which is not available through CRAN. Visit the site, or more simply
enter the following code at the prompt in R: 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 data is included in the package. The following code services as a simple vignette for using the package for now.

```
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")
```

```
## 1: -236.837262206168
## 2: -238.057618245916
## 3: -237.342529220994
## 4: -236.848450287613
## 5: -236.848450287613
## 6: -236.400242074085
## 7: -236.837262206168
## 8: -236.400242074085
## 9: -237.342529220994
## 10: -237.302667466497
```

```
inla.diploffect.summary <- run.diploffect.inla.summary.stats(inla.diploffect)
```

```
## Loading nonqtl proportion of variance explained (var components and sums of squares)...
## Loading strain effects...
## Loading additive heritability...
## Loading additive sums of squares...
## Loading deviation effects...
## Loading deviation means...
## Loading diplotype means...
## Loading dominant heritability...
## Loading total QTL heritability...
## Loading dominant sums of squares...
## Loading total QTL sums of squares...
```

```
plot.straineff.ci(inla.diploffect.summary)
```

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