R/qtl: QTL mapping in experimental crosses

R/qtl: QTL mapping in experimental crosses

Vol. 19 no. 7 2003 | Karl W. Broman, Hao Wu, Šaunak Sen, and Gary A. Churchill
R/qtl is an interactive and extensible software package designed for mapping quantitative trait loci (QTLs) in experimental crosses derived from inbred lines. It is implemented as an add-on for the freely available statistical software R, offering a comprehensive set of methods for QTL mapping, including genetic map estimation, genotyping error identification, and genome scans for single and two-QTL models. The software supports various data formats and is compatible with Windows, Unix, and MacOS. Key features include hidden Markov model (HMM) technology for handling missing genotype data, functions for visualizing and error-checking genotyping data, and multiple methods for QTL detection such as EM algorithm, Haley–Knott regression, and multiple imputation. Future developments aim to enhance higher-order QTL models, model comparison, and X chromosome handling, with plans to integrate multiple trait analysis and develop a graphical user interface.R/qtl is an interactive and extensible software package designed for mapping quantitative trait loci (QTLs) in experimental crosses derived from inbred lines. It is implemented as an add-on for the freely available statistical software R, offering a comprehensive set of methods for QTL mapping, including genetic map estimation, genotyping error identification, and genome scans for single and two-QTL models. The software supports various data formats and is compatible with Windows, Unix, and MacOS. Key features include hidden Markov model (HMM) technology for handling missing genotype data, functions for visualizing and error-checking genotyping data, and multiple methods for QTL detection such as EM algorithm, Haley–Knott regression, and multiple imputation. Future developments aim to enhance higher-order QTL models, model comparison, and X chromosome handling, with plans to integrate multiple trait analysis and develop a graphical user interface.
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