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

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 Collaborativ...

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Bibliographic Details
Published in:Genetics (Austin) 2019-02, Vol.211 (2), p.495-502
Main Authors: Broman, Karl W, Gatti, Daniel M, Simecek, Petr, Furlotte, Nicholas A, Prins, Pjotr, Sen, Śaunak, Yandell, Brian S, Churchill, Gary A
Format: Article
Language:English
Subjects:
Animals
Chromosome Mapping - methods
Collaboration
Computer programs
Design
Freeware
Gene expression
Gene mapping
Genetics
Genome-Wide Association Study - methods
Genomes
Genotype & phenotype
Genotyping
Genotyping Techniques - methods
Haplotypes
Investigations
Mapping
Mice
Nematodes
Open source software
Phenotypes
Plant populations
Population
Population structure
Populations
Programming languages
Proteomics
Quantitative Trait Loci
Single-nucleotide polymorphism
Software
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Summary: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.
ISSN:1943-2631
0016-6731
1943-2631
DOI:10.1534/genetics.118.301595