Journal
GENETICS
Volume 211, Issue 2, Pages 495-502Publisher
GENETICS SOCIETY AMERICA
DOI: 10.1534/genetics.118.301595
Keywords
software; QTL; multiparent populations; MAGIC; Diversity Outbred mice; heterogeneous stock; Collaborative Cross; Multiparent Advanced Generation Inter-Cross (MAGIC); MPP
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Funding
- National Institutes of Health [R01GM074244, R01GM070683, R01GM123489]
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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 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.
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