R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations

By Karl W. Broman, Daniel M. Gatti, Petr Simecek, Nicholas A. Furlotte, Pjotr Prins, Śaunak Sen, Brian S. Yandell, Gary A. Churchill. Genetics, 2018

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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 multiparental populations, better handles modern high-dimensional data.... 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 multiparent 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, which is free and open source software written in the R and C++ programming languages, comes with a test framework.

Subfields: Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/f6dfc4881b2aebad178985a6f6891d337075c9b3