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 (< http://www.synbreed.tum.de>). 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).


News

0.12-6

  • Uploaded on r-forge 2017 - 04 - 21

  • Addition for compatibility with objects generated with version 0.11

0.12-5

  • Uploaded on r-forge 2017 - 04 - 19

  • Fixed formatting bug in write.vcf

0.12-4

  • 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

0.12-3

  • Uploaded on r-forge 2017 - 04 - 03

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

  • bug in codeGeno fixed

0.12-2

  • Uploaded on r-forge 2017 - 03 - 28

  • Minor changes due to bug fixes

  • Ploidy option in codeGeno

0.12-1

  • Uploaded on r-forge 2017 - 03 - 27

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

0.12-0

  • 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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install.packages("synbreed")

0.12-9 by Hans-Juergen Auinger, a month ago


http://synbreed.r-forge.r-project.org/


Browse source code at https://github.com/cran/synbreed


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