Analysing Inbreeding Based on Genetic Markers.

inbreedR

Goal

inbreedR provides functions and workflows for the analysis of inbreeding and heterozygosity-fitness correlations (HFCs) based on molecular markers such as microsatellites and SNPs. In case of genomic data, it’s most useful for lower density datasets where it is unclear whether genotyped markers represent genome-wide diversity / inbreeding. It has four main application areas:

• Quantifying variance in inbreeding through estimation of identitiy disequilibria (g2), heterozygosity-heterozygosity correlations (HHC) and variance in standardized multilocus heterozygosity (sMLH)

• Calculating g2 for small and large SNP datasets. The use of data.table and parallelization speed up bootstrapping and permutation tests

• Estimating central parameters within HFC theory, such as the influence of inbreeding on heterozygosity and fitness, and their confidence intervals.

• Exploring the sensitivity of these measures towards the number of genetic markers using simulations

Installation

You can install the stable version of inbreedR from CRAN with:

install.packages("rptR")

Or the development version from GitHub with:

# install.packages("remotes")
remotes::install_github("mastoffel/inbreedR", build_vignettes = TRUE, dependencies = TRUE) 
# manual
browseVignettes("inbreedR")

If you find a bug, please report a minimal reproducible example in the issues.

Get started with inbreedR

To get started read the vignette:

vignette("inbreedR_step_by_step", package = "inbreedR")

Citation

Stoffel, M. A., Esser, M., Kardos, M., Humble, E., Nichols, H., David, P., & Hoffman, J. I. (2016). inbreedR: an R package for the analysis of inbreeding based on genetic markers. Methods in Ecology and Evolution, 7(11), 1331-1339.