A Guide to QTL Mapping with R/qtl: Online complements

Buy the book	Errata
Description	Software
Reviews	Sample data files
Contents	Contact the authors
Sample chapter (pdf)

Buy the book

Buy a copy (ISBN: 978-0-387-92124-2): Directly from the publisher, Springer. At Amazon, Borders, Barnes & Noble, Powells.

Description

Our aim in this book is to give 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 (an add-on package for R). We give some of the details of the statistical methods, but mostly focus on how to get and make sense of results. Real data examples are included throughout.

The intended audience includes scientists who are performing QTL mapping experiments and want to participate directly in the analysis. Some readers will be statisticians analyzing data from QTL experiments with a basic understanding of genetics.

All of the R code used in the book, including the detailed code used to create the figures, is available in files below, under Software. In addition, we have created an R package, R/qtlbook, that contains all of our example data sets (except those already included in R/qtl); it is also available under Software, below.

Reviews

Q Zhou (2010) Journal of Statistical Software Vol. 32, Book Review 5 [pdf (133k)]

"In sum, 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."

Contents

Detailed contents as PDF: contents.pdf

1		Introduction
2		Importing and simulating data
3		Data checking
4		Single-QTL analysis [Sample chapter (pdf)]
5		Non-normal phenotypes
6		Experimental design and power
7		Working with covariates
8		Two-dimensional, two-QTL scans
9		Fit and exploration of multiple-QTL models
10		Case study I
11		Case study II
A		Installing R and R/qtl
B		List of functions in R/qtl
C		QTL mapping data sets
D		Hidden Markov models for QTL mapping

Errata

1. Chapter 1, pages 4 and 5, legends to Fig. 1.1 and 1.2: Where we say "blue and pink", we should have said "blue and red".
2. Chapter 11, page 349, Fig. 11.14 is seriously messed up. The figure should appear as follows. (Click the image to see a larger version.)

   

Software

R web page

R/qtl web page [Download page]

R/qtlbook package (with the example data used in the book):

	Unix source:		qtlbook_0.17-3.tar.gz		(26 Oct 2009)
	Mac OS X binary:		qtlbook_0.17-3.tgz
	Windows binary:		qtlbook_0.17-3.zip

R/qtlDesign web page [Unix source (ver 0.92, 22 May 2007)]

R code from the book:

	Chapter				File(s)
	2		Importing and simulating data		chap02.R
	3		Data checking		chap03.R
	4		Single-QTL analysis		chap04.R
	5		Non-normal phenotypes		chap05.R, scanone_cph.R
	6		Experimental design and power		chap06.R
	7		Working with covariates		chap07.R
	8		Two-dimensional, two-QTL scans		chap08.R
	9		Fit and exploration of multiple-QTL models		chap09.R
	10		Case study I		chap10.R
	11		Case study II		chap11.R

Detailed R code for all figures in the book:

	Chapter				File(s)
	1		Introduction		fig01.R, meiosis_func.R
	2		Importing and simulating data		fig02.R
	3		Data checking		fig03.R
	4		Single-QTL analysis		fig04.R
	5		Non-normal phenotypes		fig05.R
	6		Experimental design and power		fig06.R
	7		Working with covariates		fig07.R
	8		Two-dimensional, two-QTL scans		fig08.R
	9		Fit and exploration of multiple-QTL models		fig09.R
	10		Case study I		fig10.R
	11		Case study II		fig11.R

All of the code from the book compressed into one file: RqtlBook_Code.tgz

Sample data files

Samples of data files for import into R/qtl, in a variety of formats and with the necessary R code, are available here.

Contact the authors

Karl W. Broman		Śaunak Sen
Department of Biostatistics and Medical Informatics		Department of Epidemiology and Biostatistics
University of Wisconsin-Madison		University of California, San Francisco
kbroman at biostat.wisc.edu		sen at biostat.ucsf.edu

Last modified: Tue Jan 19 21:31:28 CST 2010