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bioRxiv · 10.1101/414748

R/qtl2: software for mapping quantitative trait loci with high dimensional data and multi-parent populations

Broman, K. W.·Gatti, D. M.·Simecek, P.·Furlotte, N. A.·Prins, P.·Sen, S.·Yandell, B. S.·Churchill, G. A.
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Abstract

R/qtl2 is an interactive software environment for mapping quantitative trait loci (QTL) in experimental populations. The R/qtl2 software expands the scope of the widely-used R/qtl software package to include multi-parent populations derived from more than two founder strains, such as the Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations. R/qtl2 is designed to handle modern high-density genotyping data and high-dimensional molecular phenotypes including gene expression and proteomics. R/qtl2 includes the ability to perform genome scans using a linear mixed model to account for population structure, and also includes features to impute SNPs based on founder strain genomes and to carry out association mapping. The R/qtl2 software provides all of the basic features needed for QTL mapping, including graphical displays and summary reports, and it can be extended through the creation of add-on packages. R/qtl2 comes with a test framework and is free and open source software written in the R and C++ programming languages.

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Broman, K. W., Gatti, D. M., Simecek, P., Furlotte, N. A., Prins, P., Sen, S., Yandell, B. S., Churchill, G. A.. 2018-09-12. R/qtl2: software for mapping quantitative trait loci with high dimensional data and multi-parent populations. https://doi.org/10.1101/414748

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