Pedigree and Genetic Groups.

R package 'ggroups'

The official release of the package is available at CRAN: https://CRAN.R-project.org/package=ggroups

This repository contains official and development releases. To check whether the latest official and the latest development versions are different, please notice the badges on top of the page for the official (CRAN) and development (release) versions.

Installation

To get the current released version from CRAN:

install.packages("ggroups")

To get the current development version from GitHub:

# install.packages("devtools")
devtools::install_github('nilforooshan/ggroups')

Description

This package contains pedigree processing and analyzing functions, including functions for checking, extraction and renumbering the pedigree, making the additive and dominance pedigree relationship matrices and their inverses, in matrix and tabular formats, calculating inbreeding coefficients (Meuwissen & Luo, 1992), as well as functions related to genetic groups.

Details

First, it is recommended to check the pedigree data.frame with the pedcheck function. Pedigree relationship matrix and its inverse are fundamentals in the conventional and modern animal breeding. The concept of genetic groups stems from the fact that not all the unknown parents are of the same genetic level. The genetic group contribution matrix (Q) is required to weight and add genetic group effects (ĝ) to the genetic merit of animals (û), which is equal to Qĝ + û (Quaas, 1988). Calculating Q is computationally challenging, and for large pedigree, large RAM and long computational time is required. Therefore, the functions qmatL and its parallel version, qmatXL are introduced. Overlap between sire and dam genetic groups is supported.

For more details, please read the PDF manual.

Thanks.