synbreed: a framework for the analysis of genomic prediction data using R
Open Access
- 10 June 2012
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 28 (15), 2086-2087
- https://doi.org/10.1093/bioinformatics/bts335
Abstract
Summary: We present a novel R package named synbreed to derive genome-based predictions from high-throughput genotyping and large-scale phenotyping data. The package contains a comprehensive collection of functions required to fit and cross-validate genomic prediction models. All functions are embedded within the framework of a single, unified data object. Thereby a versatile genomic prediction analysis pipeline covering data processing, visualization and analysis is established within one software package. The implementation is flexible with respect to a wide range of data formats and models. The package fills an existing gap in the availability of user-friendly software for next-generation genetics research and education. Availability:synbreed is open-source and available through CRAN http://cran.r-project.org/web/packages/synbreed. The latest development version is available from R-Forge. The package synbreed is released with a vignette, a manual and three large-scale example datasets (from package synbreedData). Contact:chris.schoen@wzw.tum.de Supplementary Information: Supplementary data are available at Bioinformatics online.Keywords
This publication has 6 references indexed in Scilit:
- Genome-based prediction of testcross values in maizeTheoretical and Applied Genetics, 2011
- Genomic‐Enabled Prediction Based on Molecular Markers and Pedigree Using the Bayesian Linear Regression Package in RThe Plant Genome, 2010
- A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated IndividualsAmerican Journal of Human Genetics, 2009
- The Impact of Genetic Relationship Information on Genome-Assisted Breeding ValuesGenetics, 2007
- PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage AnalysesAmerican Journal of Human Genetics, 2007
- R/qtl: QTL mapping in experimental crossesBioinformatics, 2003