R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations-Reference-Cited by-同舟云学术

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

Published:2019-02-01 Issue:2 Volume:211 Page:495-502
ISSN:1943-2631
Container-title:Genetics
language:en
Short-container-title:

Author:

Broman Karl W¹,Gatti Daniel M²,Simecek Petr²,Furlotte Nicholas A³,Prins Pjotr⁴⁵,Sen Śaunak⁶,Yandell Brian S⁷⁸,Churchill Gary A²

Affiliation:

1. Departments of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Wisconsin 53706

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

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 multiparental populations, better handles modern high-dimensional data.... 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.

Publisher

Oxford University Press (OUP)

Subject

Genetics

Link

https://academic.oup.com/genetics/article-pdf/211/2/495/42103782/genetics0495.pdf

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