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Bioinformatics. 2012 Aug 1;28(15):2086-7. doi: 10.1093/bioinformatics/bts335. Epub 2012 Jun 10.

synbreed: a framework for the analysis of genomic prediction data using R.

Author information

1
Plant Breeding, Technische Universität München, Emil-Ramann-Straße 4, 85354 Freising, Germany.

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.

PMID:
22689388
DOI:
10.1093/bioinformatics/bts335
[Indexed for MEDLINE]

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