Framework for the Analysis of Genomic Prediction Data using R

A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (<>). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).



  • Uploaded on r-forge 2017 - 04 - 21

  • Addition for compatibility with objects generated with version 0.11


  • Uploaded on r-forge 2017 - 04 - 19

  • Fixed formatting bug in write.vcf


  • Uploaded on r-forge 2017 - 04 - 05

  • Smoothier presentation of alleles in gpData$map

  • Revised version of write.vcf(), missing positions printed for genetic positions

  • Removed links in help to packages not needed any more

  • Minor changes due to little bugs


  • Uploaded on r-forge 2017 - 04 - 03

  • Multi core calculation in pairwiseLD-function for R internal calculations

  • bug in codeGeno fixed


  • Uploaded on r-forge 2017 - 03 - 28

  • Minor changes due to bug fixes

  • Ploidy option in codeGeno


  • Uploaded on r-forge 2017 - 03 - 27

  • Parallel versions for functions create.gpData, kin, pairwiseLD, summary.LDdf, summary.LDmat


  • Uploaded on r-forge 2017 - 03 - 24

  • Parallelization of functions codeGeno, read.vcf2matrix, read.vcf2list, write.vcf

  • Allelefrequencies and alleles added to the map of gpData-object

  • beagle version 4.1 for imputation

  • Minor bug fixes

Reference manual

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0.12-9 by Hans-Juergen Auinger, 3 months ago

Browse source code at

Authors: Hans-Juergen Auinger, Valentin Wimmer, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar

Documentation:   PDF Manual  

GPL-3 license

Imports abind, BGLR, doBy, doParallel, foreach, igraph, lattice, qtl, regress, MASS, methods, LDheatmap

Suggests synbreedData

Suggested by heritability.

See at CRAN