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Genetics. 2019 Feb;211(2):495-502. doi: 10.1534/genetics.118.301595. Epub 2018 Dec 27.

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

Author information

1
Departments of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Wisconsin 53706 broman@wisc.edu.
2
The Jackson Laboratory, Bar Harbor, Maine 04609.
3
23andMe, Mountain View, California 94043.
4
Departments of Genetics, Genomics, and Informatics, University of Tennessee Health Sciences Center, Memphis, Tennessee 38163.
5
Center for Molecular Medicine, University Medical Center Utrecht, 3584CT, The Netherlands.
6
Preventive Medicine, University of Tennessee Health Sciences Center, Memphis, Tennessee 38163.
7
Horticulture Department, University of Wisconsin-Madison, Wisconsin 53706.
8
Statistics, University of Wisconsin-Madison, Wisconsin 53706.

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 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.

KEYWORDS:

Collaborative Cross; Diversity Outbred mice; MAGIC; MPP; Multiparent Advanced Generation Inter-Cross (MAGIC); QTL; heterogeneous stock; multiparent populations; software

PMID:
30591514
PMCID:
PMC6366910
DOI:
10.1534/genetics.118.301595
[Indexed for MEDLINE]
Free PMC Article

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