Foulkes Applied Statistical Genetics with R

For Population-based Association Studies
1. Auflage 2009
ISBN: 978-0-387-89554-3
Verlag: Springer
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 252 Seiten

Reihe: Use R!

Statistical genetics has become a core course in many graduate programs in public health and medicine. This book presents fundamental concepts and principles in this emerging field at a level that is accessible to students and researchers with a first course in biostatistics. Extensive examples are provided using publicly available data and the open source, statistical computing environment, R.

Autoren/Hrsg.

Foulkes, Andrea S.

Inhaltsverzeichnis

1;Preface;6
2;Contents;11
3;List of Tables;15
4;List of Figures;16
5;Acronyms;17
6;1 Genetic Association Studies;20
6.1;1.1 Overview of population-based investigations;21
6.2;1.2 Data components and terminology;26
6.3;1.3 Data examples;31
6.4;Problems;46
7;2 Elementary Statistical Principles;47
7.1;2.1 Background;48
7.2;2.2 Measures and tests of association;55
7.3;2.3 Analytic challenges;73
7.4;Problems;80
8;3 Genetic Data Concepts and Tests;82
8.1;3.1 Linkage disequilibrium (LD);82
8.2;3.2 Hardy-Weinberg equilibrium (HWE);95
8.3;3.3 Quality control and preprocessing;103
8.4;Problems;112
9;4 Multiple Comparison Procedures;114
9.1;4.1 Measures of error;114
9.2;4.2 Single-step and step-down adjustments;118
9.3;4.3 Resampling-based methods;131
9.4;4.4 Alternative paradigms;140
9.5;Problems;144
10;5 Methods for Unobservable Phase;146
10.1;5.1 Haplotype estimation;147
10.2;5.2 Estimating and testing for haplotype{trait association;157
10.3;Problems;166
10.4;Supplemental notes;167
10.5;Supplemental R scripts;172
11;6 Classification and Regression Trees;174
11.1;6.1 Building a tree;174
11.2;6.2 Optimal trees;190
11.3;Problems;196
12;7 Additional Topics in High-Dimensional Data Analysis;197
12.1;7.1 Random forests;198
12.2;7.2 Logic regression;214
12.3;7.3 Multivariate adaptive regression splines;221
12.4;7.4 Bayesian variable selection;225
12.5;7.5 Further readings;227
12.6;Problems;228
13;Appendix R Basics;229
13.1;A.1 Getting started;229
13.2;A.2 Types of data objects;232
13.3;A.3 Importing data;236
13.4;A.4 Managing data;237
13.5;A.5 Installing packages;240
13.6;A.6 Additional help;241
14;References;242
15;Glossary of Terms;251
16;Glossary of Select R Packages;256
17;Subject Index;259
18;Index of R Functions and Packages;263