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

Karl W Broman, Daniel M. Gatti, Petr Simecek, Nicholas A. Furlotte, Pjotr Prins, Saunak Sen, Brian S. Yandell, Gary A. Churchill
2018 biorxiv/medrxiv   pre-print
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
more » ... ding 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.
doi:10.1101/414748 fatcat:y7xlwobjgzeyniqdetdcscqnze