A Guide to QTL Mapping with R/qtl
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, interac
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Karl W. Broman S´ aunak Sen
A Guide to QTL Mapping with R/qtl
Statistics for Biology and Health Series M. Gail K. Krickeberg J. Samet A. Tsiatis W. Wong
For other titles published in this series, go to http://www.springer.com/series/2848
´ Karl W. Broman · Saunak Sen
A Guide to QTL Mapping with R/qtl
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Karl W. Broman Department of Biostatistics & Medical Informatics University of Wisconsin–Madison 1300 University Ave. Madison, WI 53706-1510 USA [email protected]
´ Saunak Sen Department of Epidemiology & Biostatistics University of California, San Francisco 185 Berry St., Suite 5700 San Francisco, CA 94107-1762 USA [email protected]
Portions of the authors’ articles published in Genetics are reprinted with permission of the Genetics Society of America. R is a registered trademark of Linus Torvalds. Linux
GoogleTM and Google GroupsTM are trademarks of Google Inc. R R R Microsoft , Windows , and Excel are registered trademarks of Microsoft Corporation. R R R Mac , Mac OS , and Macintosh are registered trademarks of Apple Computer, Inc. R UNIX is a registered trademark of The Open Group.
ISSN 1431-8776 ISBN 978-0-387-92124-2 e-ISBN 978-0-387-92125-9 DOI 10.1007/978-0-387-92125-9 Springer Dordrecht Heidelberg London New York Library of Congress Control Number: 2009929238 c Springer Science+Business Media, LLC 2009 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com)
To Aimee and Suheeta
Preface
QTL are quantitative trait loci: genetic loci that contribute to variation in a quantitative trait. QTL mapping is the effort to identify QTL through an experimental cross. In this book, we 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 the general statistical software, R). We give some of the details of the statistical methods, but we 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 participating directly in the analysis. We expect the reader to have a general understanding of statistical methods, including maximum likelihood estimation and linear
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