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README.md

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.

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.

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R functions related to pedigrees

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