A Guide to QTL Mapping with R/qtl (Statistics for Biology and Health)

Quantitative trait locus (QTL) mapping is used to discover the genetic and molecular architecture underlying complex quantitative traits. It has important applications in agricultural, evolutionary, and biomedical research. R/qtl is an extensible, interactive environment for QTL mapping in experimental crosses. It is implemented as a package for the widely used open source statistical software R and contains a diverse array of QTL mapping methods, diagnostic tools for ensuring high-quality data, and facilities for the fit and exploration of multiple-QTL models, including QTL x QTL and QTL x environment interactions. This book is a comprehensive guide to the practice of QTL mapping and the use of R/qtl, including study design, data import and simulation, data diagnostics, interval mapping and generalizations, two-dimensional genome scans, and the consideration of complex multiple-QTL models. Two moderately challenging case studies illustrate QTL analysis in its entirety. The book alternates between QTL mapping theory and examples illustrating the use of R/qtl. Novice readers will find detailed explanations of the important statistical concepts and, through the extensive software illustrations, will be able to apply these concepts in their own research. Experienced readers will find details on the underlying algorithms and the implementation of extensions to R/qtl. There are 150 figures, including 90 in full color. Karl W. Broman is Professor in the Department of Biostatistics and Medical Informatics at the University of Wisconsin-Madison, and is the chief developer of R/qtl. Saunak Sen is Associate Professor in Residence in the Department of Epidemiology and Biostatistics and the Center for Bioinformatics and Molecular Biostatistics at the University of California, San Francisco. Front Matter....Pages i-xii Introduction....Pages 1-20 Importing and simulating data....Pages 21-46 Data checking....Pages 47-73 Single-QTL analysis....Pages 75-133 Non-normal phenotypes....Pages 135-151 Experimental design and power....Pages 153-177 Working with covariates....Pages 179-211 Two-dimensional, two-QTL scans....Pages 213-239 Fit and exploration of multiple-QTL models....Pages 241-282 Case study I....Pages 283-312 Case study II....Pages 313-354 Back Matter....Pages 1-40 A guide to the practice of quantitative trait locus (QTL) mapping and the use of R/qtl, an interactive environment for QTL mapping in experimental crosses. It includes study design, data import and simulation, data diagnostics, interval mapping and generalizations, two-dimensional genome scans, and the consideration of complex multiple-QTL models

Comprehensive discussion of QTL mapping concepts and theory

Detailed instructions on the use of the R/qtl software, the most featured and flexible software for QTL mapping

Two case studies illustrate QTL analysis in its entirety

This volume gives an overview of the practical aspects of the analysis of QTL mapping experiments based on inbred line crosses, with explicit instructions on the use of the R/qtl software