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

被引：267

作者：

Broman, Karl W. ^{[1
]}

Gatti, Daniel M. ^{[4
]}

Simecek, Petr ^{[4
]}

Furlotte, Nicholas A. ^{[5
]}

Prins, Pjotr ^{[6
,8
]}

Sen, Saunak ^{[2
,7
]}

Yandell, Brian S. ^{[3
]}

Churchill, Gary A. ^{[4
]}

机构：

[1] Univ Wisconsin, Dept Biostat & Med Informat, Madison, WI 53706 USA

[2] Univ Wisconsin, Dept Hort, 1575 Linden Dr, Madison, WI 53706 USA

[3] Univ Wisconsin, Dept Stat, Madison, WI 53706 USA

[4] Jackson Lab, 600 Main St, Bar Harbor, ME 04609 USA

[5] 23andMe, Mountain View, CA 94043 USA

[6] Univ Tennessee, Ctr Hlth Sci, Dept Genet Genom & Informat, Memphis, TN 38163 USA

[7] Univ Tennessee, Ctr Hlth Sci, Dept Prevent Med, Memphis, TN 38163 USA

[8] Univ Med Ctr Utrecht, Ctr Mol Med, NL-3584 CT Utrecht, Netherlands

来源：

GENETICS | 2019年 / 211卷 / 02期

基金：

美国国家卫生研究院;

关键词：

software; QTL; multiparent populations; MAGIC; Diversity Outbred mice; heterogeneous stock; Collaborative Cross; Multiparent Advanced Generation Inter-Cross (MAGIC); MPP; MODEL SELECTION APPROACH; GENETIC-ANALYSIS; COLLABORATIVE CROSS; R PACKAGE; QTL; DISCOVERY; IDENTIFICATION; PROBABILITIES; SEQUENCE; PLATFORM;

D O I：

10.1534/genetics.118.301595

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

引用

页码：495 / 502

页数：8

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