R/qtl: high-throughput multiple QTL mapping

Danny Arends, Pjotr Prins, Ritsert C. Jansen, Karl W. Broman

Research output: Contribution to journalArticlepeer-review

284 Citations (Scopus)


Motivation: R/qtl is free and powerful software for mapping and exploring quantitative trait loci (QTL). R/qtl provides a fully comprehensive range of methods for a wide range of experimental cross types. We recently added multiple QTL mapping (MQM) to R/qtl. MQM adds higher statistical power to detect and disentangle the effects of multiple linked and unlinked QTL compared with many other methods. MQM for R/qtl adds many new features including improved handling of missing data, analysis of 10 000 s of molecular traits, permutation for determining significance thresholds for QTL and QTL hot spots, and visualizations for cis–trans and QTL interaction effects. MQM for R/qtl is the first free and open source implementation of MQM that is multi-platform, scalable and suitable for automated procedures and large genetical genomics datasets.Availability: R/qtl is free and open source multi-platform software for the statistical language R, and is made available under the GPLv3 license. R/qtl can be installed from http://www.rqtl.org/. R/qtl queries should be directed at the mailing list, see http://www.rqtl.org/list/.Contact:kbroman@biostat.wisc.edu
Original languageEnglish
Pages (from-to)2990-2992
Number of pages3
Issue number23
Publication statusPublished - 1 Oct 2010
Externally publishedYes


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