Guide to QTL Mapping with R/qtl

From the reviews: "The book by Broman and Sen gives a practical review of statistical QTL mapping in experimental crosses with step-by-step instructions to the use of the R package qtl. ...has a wide coverage of topics, from experimental design and data input, to single-QTL mapping, mapping with covariates and multiple-GTL scans, organized into 11 chapters according to the logic flow of a QTL analysis. The authors made a good compromise between statistical methodology and real-data illustration with R code, so that different readers may easily focus on the parts that are more interesting to them. A researcher can follow the code in the examples of the book to study real-data applications of the qtl package. ...this is a well-written book with carefully chosen and nicely organized topics. It can serve as a good introduction to QTL mapping methodology and a useful practical guide to the R package. ..." (Journal of Statistical Software, Vol. 32, Book Review 5, January 2010) "The book gives an overview of the practical aspects of the analysis of QTL mapping experiments ... . Most of the chapters start with a short introduction and finish with a summary and suggestions of further reading listing numerous review articles connected with the discussed subject. ... There are 150 figures, including 90 in full color. We recommend it, first of all, to scientists who use QTL mapping analysis, and also to postdoctoral researchers and graduated students interested in exploring applications of statistics."--- (I. Czyczylo-Mysza and I. Marcinska, Acta Physiologiae Plantarum, Vol. 32, March, 2010)

• Importing and simulating data.- Data checking.- Single-QTL analysis.- Non-normal phenotypes.- Experimental design and power.- Working with covariates.- Two-dimensional, two-QTL scans.- Fit and exploration of multiple-QTL models.- Case study I.- Case study II.