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 2013 - 09 - 19

  • updated dependency from igraph0 to igraph


  • Uploaded on R-Forge 2013 - 03 - 18

  • Updated maize centromere positions according to maizeGDB, version 2

  • Fixed bug in add.individuals

  • Added option in codeGeno to code by a reference allele for each marker

  • Option to supply user-specified values instead of the MAF to correct in function kin for ret="realized" and ret="realizedAB" (thanks to Yvonne Badke for this suggestion)

  • Fixed bug in crossVal when committing a TS


  • Uploaded on R-Forge 2013 - 03 - 15

  • Added warning in case of large entries in the inverse covariance matrix of crossVal

  • Return original alleles in write.beagle, not only "A" and "B" by default in the marker file

  • Added summary method for LDmat and LDdf

  • Fixed bugs in write.beagle and codeGeno (counting number of missing values with Beagle)

  • Include lowest category for r2 and dist breaks in LDDist and plot.LDdf

  • changed function .path.package to path.package


  • Uploaded on CRAN 2012 - 09 - 20

  • Bug fix in create.gpData() to get full compatibility with write.plink() and other functions

  • In plot functions and LDDist and LDMap the format "png" is now available for graphic files. For fileType = "pdf" the option oneFile is added.

  • new class 'GenMap' for marker maps

  • generic plot functions for classes LDdf and LDmat. Decision can be made between "dist" and "map" respectively and for both "neighbour"

  • search for duplicated IDs in create.gpData()

  • fixed bug in feature of codeGeno when non-numeric coded genotypes were used

  • Included citation file


  • Uploaded on CRAN 2012 - 05 - 24

  • Included default value for gpData$covar$family to avoid an error when running write.plink without family information, replaced error by a warning (on R-Forge since 2012 - 03 - 28)

  • Included addtional '' argument for function codeGeno to generate (optionally) a report to decode original coding scheme, and count number of missing values per SNP

  • Bug fix in codeGeno using family imputing, polymorphic families were identified partly incorrect

  • Bug fix in predict.gpMod, when using BLUP and marker effects (on R-Forge since 2012-05-04)

  • Renamed return argument in gpMod: predicton -> prediction

  • Added argument 'ld.window' to function pairwiseLD (on R-Forge since 2012-05-07)

  • Changed dependency: igraph -> igraph0 (on R-Forge since 2012-05-10)

  • Improved color key representation for plotGenMap (on R-Forge since 2012-05-22)

  • Report of mean values for the diagonal/off-diagonal in summary.relationshipMatrix


  • Uploaded on CRAN 2012 - 03 - 22

  • updated vignette, replace LDmaize.pdf by LDmaize.png

  • proof-reading of the manual

  • minor updates in the demos

Reference manual

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0.12-6 by Hans-Juergen Auinger, 7 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, grid, igraph, lattice, LDheatmap, MASS, methods, parallel, qtl, regress

Suggests synbreedData

Suggested by heritability.

See at CRAN