README.md

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. 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

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)

gkeele/Diploffect.INLA documentation built on May 17, 2023, 8:37 a.m.