README.md

In Rpedigree/pedigreeR: Versatile Functions for Working with Pedigrees

pedigreeTools

The pedigreeTools package offers a suit of functions for pedigree analyses, including: sorting and editing pedigree data, computing inbreeding, additive relationships and functions of it (e.g., cholesky derived from a pedigree, inverse of a numerator relationship matrix). The package was originally co-developed by Douglas M. Bates and Ana I. Vazquez and was incorporated in the lme4 R-package. Recently, pedigreeTools evolved to an stand-alone package. We have added new features for pedigree edition, analysis of data from self-pollination and for subsetting pedigrees.

Developers: Ana I. Vazquez, Douglas M. Bates, Paulino Perez-Rodriguez, G. de los Campos, S. Avadhanam & Gregor Gorjanc

Installing pedigreeTools from GitHub

#R functions related to pedigrees
install.packages(pkg='devtools',repos='https://cran.r-project.org/')  #1# install devtools
library(devtools)                                                     #2# load the library
install_git('https://github.com/Rpedigree/pedigreeTools/')            #3# install pedigreeTools from GitHub

Examples

1. Completing and sorting a pedigree.
2. Computing inbreeding, additive relationships and funcitons of it.
3. Subsetting a Pedigree using prunePed.
4. Pedigree analyses for self-pollinated species.
5. Cross-validation analyses with pedigreeTools and pedigreemm.

Rpedigree/pedigreeR documentation built on Oct. 13, 2023, 7:35 p.m.