R programming for bioinformatics.pdf

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Title

Contents

Chapter 1: Introducing R

Chapter 2: R Language Fundamentals

Chapter 3: Object-Oriented Programming in R

Chapter 4: Input and Output in R

Chapter 5: Working with Character Data

Chapter 6: Foreign Language Interfaces

Chapter 7: R Packages

Chapter 8: Data Technologies

Chapter 9: Debugging and Profiling

References

Index

R Programming for Bioinformatics

Chapman & Hall/CRC Computer Science and Data Analysis Series The interface between the computer and statistical sciences is increasing, as each discipline seeks to harness the power and resources of the other. This series aims to foster the integration between the computer sciences and statistical, numerical, and probabilistic methods by publishing a broad range of reference works, textbooks, and handbooks. SERIES EDITORS David Blei, Princeton University David Madigan, Rutgers University Marina Meila, University of Washington Fionn Murtagh, Royal Holloway, University of London Proposals for the series should be sent directly to one of the series editors above, or submitted to: Chapman & Hall/CRC 4th Floor, Albert House 1-4 Singer Street London EC2A 4BQ UK Published Titles Bayesian Articial Intelligence Kevin B. Korb and Ann E. Nicholson Computational Statistics Handbook with MATLAB®, Second Edition Wendy L. Martinez and Angel R. Martinez Pattern Recognition Algorithms for Data Mining Sankar K. Pal and Pabitra Mitra Exploratory Data Analysis with MATLAB® Wendy L. Martinez and Angel R. Martinez Clustering for Data Mining: A Data Recovery Approach Boris Mirkin Correspondence Analysis and Data Coding with Java and R Fionn Murtagh Design and Modeling for Computer Experiments Kai-Tai Fang, Runze Li, and Agus Sudjianto Introduction to Machine Learning and Bioinformatics Sushmita Mitra, Sujay Datta, Theodore Perkins, and George Michailidis R Graphics Paul Murrell R Programming for Bioinformatics Robert Gentleman Semisupervised Learning for Computational Linguistics Steven Abney Statistical Computing with R Maria L. Rizzo

R Programming for Bioinformatics Robert Gentleman Fred Hutchinson Cancer Research Center Seattle, Washington, U.S.A.

Chapman & Hall/CRC Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2009 by Taylor & Francis Group, LLC Chapman & Hall/CRC is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Printed in the United States of America on acid-free paper 10 9 8 7 6 5 4 3 2 1 International Standard Book Number-13: 978-1-4200-6367-7 (Hardcover) This book contains information obtained from authentic and highly regarded sources Reason- able efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The Authors and Publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, please access www. copyright.com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC) 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that provides licenses and registration for a variety of users. For organizations that have been granted a photocopy license by the CCC, a separate system of payment has been arranged. Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe. Library of Congress Cataloging-in-Publication Data Gentleman, Robert, 1959- R programming for bioinformatics / Robert Gentleman. p. cm. -- (Chapman & Hall/CRC computer science and data analysis series) Bibliographical references (p. ) and index. ISBN 978-1-4200-6367-7 1. Bioinformatics. 2. R (Computer program language) I. Title. II. Series. QH324.2.G46 2008 572.80285’5133--dc22 Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com 2008011352

To Tanja, Sophie and Katja

Contents 1 Introducing R 1.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.2 Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.3 A note on the text . . . . . . . . . . . . . . . . . . . . . . . . 1.4 Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . 2 R Language Fundamentals 2.1 Some special values 2.3.1 Finding out more about an object Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.1.1 A brief introduction to R . . . . . . . . . . . . . . . . 2.1.2 Attributes . . . . . . . . . . . . . . . . . . . . . . . . . 2.1.3 A very brief introduction to OOP in R . . . . . . . . . 2.1.4 . . . . . . . . . . . . . . . . . . . 2.1.5 Types of objects . . . . . . . . . . . . . . . . . . . . . 2.1.6 Sequence generating and vector subsetting . . . . . . . 2.1.7 Types of functions . . . . . . . . . . . . . . . . . . . . 2.2 Data structures . . . . . . . . . . . . . . . . . . . . . . . . . . 2.2.1 Atomic vectors . . . . . . . . . . . . . . . . . . . . . . 2.2.2 Numerical computing . . . . . . . . . . . . . . . . . . 2.2.3 Factors . . . . . . . . . . . . . . . . . . . . . . . . . . 2.2.4 Lists, environments and data frames . . . . . . . . . . 2.3 Managing your R session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.4 Language basics . . . . . . . . . . . . . . . . . . . . . . . . . . 2.4.1 Operators . . . . . . . . . . . . . . . . . . . . . . . . . 2.5 Subscripting and subsetting . . . . . . . . . . . . . . . . . . . 2.5.1 Vector and matrix subsetting . . . . . . . . . . . . . . 2.6 Vectorized computations . . . . . . . . . . . . . . . . . . . . . 2.6.1 The recycling rule . . . . . . . . . . . . . . . . . . . . 2.7 Replacement functions . . . . . . . . . . . . . . . . . . . . . . 2.8 Functional programming . . . . . . . . . . . . . . . . . . . . . 2.9 Writing functions . . . . . . . . . . . . . . . . . . . . . . . . . 2.10 Flow control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.11 Exception handling . . . . . . . . . . . . . . . . . . . . . . . . 2.12 Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.12.1 Standard evaluation . . . . . . . . . . . . . . . . . . . 2.12.2 Non-standard evaluation . . . . . . . . . . . . . . . . . 2.10.1 Conditionals 1 1 2 3 4 5 5 5 6 7 8 9 11 12 12 12 15 16 18 22 24 25 26 28 29 36 37 38 39 41 42 44 45 50 51 52 vii

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