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Open Access Technical Note

qtl.outbred: Interfacing outbred line cross data with the R/qtl mapping software

Ronald M Nelson1*, Xia Shen2 and Örjan Carlborg12

Author Affiliations

1 Department of Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-75007 Uppsala, Sweden

2 Department of Cell and Molecular Biology, Uppsala University, BMC Box 598, SE-75124 Uppsala, Sweden

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BMC Research Notes 2011, 4:154  doi:10.1186/1756-0500-4-154

Published: 26 May 2011

Abstract

Background

qtl.outbred is an extendible interface in the statistical environment, R, for combining quantitative trait loci (QTL) mapping tools. It is built as an umbrella package that enables outbred genotype probabilities to be calculated and/or imported into the software package R/qtl.

Findings

Using qtl.outbred, the genotype probabilities from outbred line cross data can be calculated by interfacing with a new and efficient algorithm developed for analyzing arbitrarily large datasets (included in the package) or imported from other sources such as the web-based tool, GridQTL.

Conclusion

qtl.outbred will improve the speed for calculating probabilities and the ability to analyse large future datasets. This package enables the user to analyse outbred line cross data accurately, but with similar effort than inbred line cross data.