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Genetics. 2018 Dec 27. pii: genetics.301595.2018. doi: 10.1534/genetics.118.301595. [Epub ahead of print]

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

Author information

1
University of Wisconsin-Madison broman@wisc.edu.
2
The Jackson Laboratory.
3
23andMe.
4
University of Tennessee Health Sciences Center; University Medical Center Utrecht.
5
University of Tennessee Health Science Center.
6
University of Wisconsin-Madison.

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.

KEYWORDS:

Collaborative Cross; Diversity Outbred mice; MAGIC; QTL; heterogeneous stock; multi-parent populations; software

PMID:
30591514
DOI:
10.1534/genetics.118.301595
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