R/qtl: high-throughput multiple QTL mapping.

Authors :: Arends D
Prins P
Jansen RC
Broman KW
Source :: Bioinformatics (Oxford, England) [Bioinformatics] 2010 Dec 01; Vol. 26 (23), pp. 2990-2. Date of Electronic Publication: 2010 Oct 21.
Publication Year :: 2010
Abstract: 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.<br />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/.<br />Contact: kbroman@biostat.wisc.edu.