publication . Article . Preprint . Other literature type . 2018

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

Gary A. Churchill; Nicholas A. Furlotte; Brian S. Yandell; Daniel M. Gatti; Pjotr Prins; Pjotr Prins; Śaunak Sen; Karl W. Broman; Petr Simecek;
Open Access English
  • Published: 12 Sep 2018 Journal: Genetics, volume 211, issue 2, pages 495-502 (issn: 0016-6731, eissn: 1943-2631, Copyright policy)
  • Publisher: Genetics Society of America
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...
Subjects
free text keywords: Investigations, Multiparental Populations, software, QTL, multiparent populations, MAGIC, Diversity Outbred mice, heterogeneous stock, Collaborative Cross, Multiparent Advanced Generation Inter-Cross (MAGIC), MPP, Genetics, Single-nucleotide polymorphism, Mixed model, Genotyping, business.industry, business, Genome, Clustering high-dimensional data, Computer science, Quantitative trait locus, Association mapping, Computational biology, Software package, Biology
Related Organizations
Funded by
NIH| QTL Analysis in Combined Inbred Line Crosses
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM070683-04
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NIH| Statistical Methods and Software for QTL Mapping
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM074244-06
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NIH| A Unified High Performance Web Service for Systems Genetics and Precision Medicine
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R01GM123489-01A1
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
63 references, page 1 of 5

Albert F. W.Kruglyak L., 2015 The role of regulatory variation in complex traits and disease.Nat. Rev. Genet.16: 197–212. 10.1038/nrg3891 25707927 [OpenAIRE] [PubMed] [DOI]

Arends D.Prins P.Jansen R. C.Broman K. W., 2010 R/qtl: high-throughput multiple QTL mapping.Bioinformatics 26: 2990–2992. 10.1093/bioinformatics/btq565 20966004 [OpenAIRE] [PubMed] [DOI]

Arends D.Li Y.Brockmann G. A.Jansen R. C.Williams R. W., 2016 Correlation trait loci (CTL) mapping: phenotype network inference subject to genotype.J. Open Source Softw.1: 87 10.21105/joss.00087 [OpenAIRE] [DOI]

Bandillo N.Raghavan C.Muyco P. A.Sevilla M. A.Lobina I. T., 2013 Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding.Rice (N. Y.)6: 11 10.1186/1939-8433-6-11 24280183 [OpenAIRE] [PubMed] [DOI]

Basten C. J.Weir B. S.Zeng Z.-B., 2002 QTL Cartographer, Version 1.16. Department of Statistics, North Carolina State University, Raleigh, NC.

Bates D.Eddelbuettel D., 2013 Fast and elegant numerical linear algebra using the RcppEigen package.J. Stat. Softw.52: 1–24. 10.18637/jss.v052.i05 23761062 [OpenAIRE] [PubMed] [DOI]

Broman K. W., 2005 The genomes of recombinant inbred lines.Genetics 169: 1133–1146. 10.1534/genetics.104.035212 15545647 [OpenAIRE] [PubMed] [DOI]

Broman K. W., 2012 a Genotype probabilities at intermediate generations in the construction of recombinant inbred lines.Genetics 190: 403–412. 10.1534/genetics.111.132647 22345609 [OpenAIRE] [PubMed] [DOI]

Broman K. W., 2012 b Haplotype probabilities in advanced intercross populations.G3 (Bethesda)2: 199–202. 10.1534/g3.111.001818 22384398 [OpenAIRE] [PubMed] [DOI]

Broman K. W., 2014 Fourteen years of R/qtl: just barely sustainable.J. Open Res. Softw.2: e11 10.5334/jors.at 25364504 [OpenAIRE] [PubMed] [DOI]

Broman K. W., 2015 R/qtlcharts: interactive graphics for quantitative trait locus mapping.Genetics 199: 359–361. 10.1534/genetics.114.172742 25527287 [OpenAIRE] [PubMed] [DOI]

Broman K. W.Sen S., 2009 A Guide to QTL Mapping with R/qtl. Springer, New York 10.1007/978-0-387-92125-9 [OpenAIRE] [DOI]

Broman K. W.Speed T. P., 2002 A model selection approach for the identification of quantitative trait loci in experimental crosses.J. R. Stat. Soc. B 64: 641–656. 10.1111/1467-9868.00354 [OpenAIRE] [DOI]

Broman K. W.Wu H.Sen S.Churchill G. A., 2003 R/qtl: QTL mapping in experimental crosses.Bioinformatics 19: 889–890. 10.1093/bioinformatics/btg112 12724300 [OpenAIRE] [PubMed] [DOI]

Broman K. W.Sen S.Owens S. E.Manichaikul A.Southard-Smith E., 2006 The X chromosome in quantitative trait locus mapping.Genetics 174: 2151–2158. 10.1534/genetics.106.061176 17028340 [OpenAIRE] [PubMed] [DOI]

63 references, page 1 of 5
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...
Subjects
free text keywords: Investigations, Multiparental Populations, software, QTL, multiparent populations, MAGIC, Diversity Outbred mice, heterogeneous stock, Collaborative Cross, Multiparent Advanced Generation Inter-Cross (MAGIC), MPP, Genetics, Single-nucleotide polymorphism, Mixed model, Genotyping, business.industry, business, Genome, Clustering high-dimensional data, Computer science, Quantitative trait locus, Association mapping, Computational biology, Software package, Biology
Related Organizations
Funded by
NIH| QTL Analysis in Combined Inbred Line Crosses
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM070683-04
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NIH| Statistical Methods and Software for QTL Mapping
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM074244-06
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NIH| A Unified High Performance Web Service for Systems Genetics and Precision Medicine
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R01GM123489-01A1
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
63 references, page 1 of 5

Albert F. W.Kruglyak L., 2015 The role of regulatory variation in complex traits and disease.Nat. Rev. Genet.16: 197–212. 10.1038/nrg3891 25707927 [OpenAIRE] [PubMed] [DOI]

Arends D.Prins P.Jansen R. C.Broman K. W., 2010 R/qtl: high-throughput multiple QTL mapping.Bioinformatics 26: 2990–2992. 10.1093/bioinformatics/btq565 20966004 [OpenAIRE] [PubMed] [DOI]

Arends D.Li Y.Brockmann G. A.Jansen R. C.Williams R. W., 2016 Correlation trait loci (CTL) mapping: phenotype network inference subject to genotype.J. Open Source Softw.1: 87 10.21105/joss.00087 [OpenAIRE] [DOI]

Bandillo N.Raghavan C.Muyco P. A.Sevilla M. A.Lobina I. T., 2013 Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding.Rice (N. Y.)6: 11 10.1186/1939-8433-6-11 24280183 [OpenAIRE] [PubMed] [DOI]

Basten C. J.Weir B. S.Zeng Z.-B., 2002 QTL Cartographer, Version 1.16. Department of Statistics, North Carolina State University, Raleigh, NC.

Bates D.Eddelbuettel D., 2013 Fast and elegant numerical linear algebra using the RcppEigen package.J. Stat. Softw.52: 1–24. 10.18637/jss.v052.i05 23761062 [OpenAIRE] [PubMed] [DOI]

Broman K. W., 2005 The genomes of recombinant inbred lines.Genetics 169: 1133–1146. 10.1534/genetics.104.035212 15545647 [OpenAIRE] [PubMed] [DOI]

Broman K. W., 2012 a Genotype probabilities at intermediate generations in the construction of recombinant inbred lines.Genetics 190: 403–412. 10.1534/genetics.111.132647 22345609 [OpenAIRE] [PubMed] [DOI]

Broman K. W., 2012 b Haplotype probabilities in advanced intercross populations.G3 (Bethesda)2: 199–202. 10.1534/g3.111.001818 22384398 [OpenAIRE] [PubMed] [DOI]

Broman K. W., 2014 Fourteen years of R/qtl: just barely sustainable.J. Open Res. Softw.2: e11 10.5334/jors.at 25364504 [OpenAIRE] [PubMed] [DOI]

Broman K. W., 2015 R/qtlcharts: interactive graphics for quantitative trait locus mapping.Genetics 199: 359–361. 10.1534/genetics.114.172742 25527287 [OpenAIRE] [PubMed] [DOI]

Broman K. W.Sen S., 2009 A Guide to QTL Mapping with R/qtl. Springer, New York 10.1007/978-0-387-92125-9 [OpenAIRE] [DOI]

Broman K. W.Speed T. P., 2002 A model selection approach for the identification of quantitative trait loci in experimental crosses.J. R. Stat. Soc. B 64: 641–656. 10.1111/1467-9868.00354 [OpenAIRE] [DOI]

Broman K. W.Wu H.Sen S.Churchill G. A., 2003 R/qtl: QTL mapping in experimental crosses.Bioinformatics 19: 889–890. 10.1093/bioinformatics/btg112 12724300 [OpenAIRE] [PubMed] [DOI]

Broman K. W.Sen S.Owens S. E.Manichaikul A.Southard-Smith E., 2006 The X chromosome in quantitative trait locus mapping.Genetics 174: 2151–2158. 10.1534/genetics.106.061176 17028340 [OpenAIRE] [PubMed] [DOI]

63 references, page 1 of 5
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