R/qtl: high-throughput multiple QTL mapping

• Published in: Bioinformatics 2010-12, Vol.26 (23), p.2990-2992
• Main Authors: Arends, Danny, Prins, Pjotr, Jansen, Ritsert C., Broman, Karl W.
• Format: Article
• Language: English
• Subjects: Applications Note; Biological and medical sciences; Chromosome Mapping - methods; experimental crosses; Fundamental and applied biological sciences. Psychology; General aspects; Genomics; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Quantitative Trait Loci; Software
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btq565

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: [e-mail]