R Programming for Bioinformatics

by Gentleman; Robert

ISBN13: 9781420063677

ISBN10: 1420063677

Format: Hardcover

Pub. Date: 2008-07-14

Publisher(s): Chapman & Hall/

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Summary

Â From the co-developer of R and lead founder of the Bioconductor ProjectThanks to its data handling and modeling capabilities and its flexibility, R is becoming the most widely used software in bioinformatics. R Programming for Bioinformaticsbuilds the programming skills needed to use R for solving bioinformatics and computational biology problems.Drawing on the author's experiences as an R expert, the book begins with coverage on the general properties of the R language, several unique programming aspects of R, and object-oriented programming in R. It presents methods for data input and output as well as database interactions. The author also examines different facets of string handling and manipulations, discusses the interfacing of R with other languages, and describes how to write software packages. He concludes with a discussion on the debugging and profiling of R code.

Introduction R	p. 1
Introduction	p. 1
Motivation	p. 2
A note on the text	p. 3
Acknowledgments	p. 4
R Language Fundamentals	p. 5
Introduction	p. 5
A brief introduction to R	p. 5
Attributes	p. 6
A very brief introduction to OOP in R	p. 7
Some special values	p. 8
Types of objects	p. 9
Sequence generating and vector subsetting	p. 11
Types of functions	p. 12
Data structures	p. 12
Atomic vectors	p. 12
Numerical computing	p. 15
Factors	p. 16
Lists, environments and data frames	p. 18
Managing your R session	p. 22
Finding out more about an object	p. 24
Language basics	p. 25
Operators	p. 26
Subscripting and subsetting	p. 28
Vector and matrix subsetting	p. 29
Vectorized computations	p. 36
The recycling rule	p. 37
Replacement functions	p. 38
Functional programming	p. 39
Writing functions	p. 41
Flow control	p. 42
Conditionals	p. 44
Exception handling	p. 45
Evaluation	p. 50
Standard evaluation	p. 51
Non-standard evaluation	p. 52
Function evaluation	p. 53
Indirect function invocation	p. 54
Evaluation on exit	p. 54
Other topics	p. 55
Name spaces	p. 57
Lexical scope	p. 59
Likelihoods	p. 61
Function optimization	p. 62
Graphics	p. 64
Object-Oriented Programming in R	p. 67
Introduction	p. 67
The basics of OOP	p. 68
Inheritance	p. 69
Dispatch	p. 71
Abstract data types	p. 72
Self-describing data	p. 73
S3 OOP	p. 74
Implicit classes	p. 76
Expression data example	p. 77
S3 generic functions and methods	p. 78
Details of dispatch	p. 81
Group generics	p. 83
S3 replacement methods	p. 83
S4 OOP	p. 84
Classes	p. 85
Types of classes	p. 98
Attributes	p. 98
Class unions	p. 99
Accessor functions	p. 100
Using S3 classes with S4 classes	p. 100
S4 generic functions and methods	p. 101
The syntax of method declaration	p. 105
The semantics of method invocation	p. 106
Replacement methods	p. 107
Finding methods	p. 107
Advanced topics	p. 108
Using classes and methods in packages	p. 110
Documentation	p. 110
Finding documentation	p. 110
Writing documentation	p. 111
Debugging	p. 111
Managing S3 and S4 together	p. 112
Getting and setting the class attribute	p. 113
Mixing S3 and S4 methods	p. 114
Navigating the class and method hierarchy	p. 115
Input and Output in R	p. 119
Introduction	p. 119
Basic file handling	p. 120
Viewing files	p. 124
File manipulation	p. 125
Working with R's binary format	p. 129
Connections	p. 130
Text connections	p. 131
Interprocess communications	p. 133
Seek	p. 136
File input and output	p. 137
Reading rectangular data	p. 138
Writing data	p. 139
Debian Control Format (DCF)	p. 140
FASTA Format	p. 141
Source and sink: capturing R output	p. 142
Tools for accessing files on the Internet	p. 143
Working with Character Data	p. 145
Introduction	p. 145
Builtin capabilities	p. 146
Modifying text	p. 151
Sorting and comparing	p. 152
Matching a set of alternatives	p. 153
Formatting text and numbers	p. 155
Special characters and escaping	p. 155
Parsing and deparsing	p. 158
Plotting with text	p. 159
Locale and font encoding	p. 159
Regular expressions	p. 159
Regular expression basics	p. 160
Matching	p. 166
Using regular expressions	p. 167
Globbing and regular expressions	p. 169
Prefixes, suffixes and substrings	p. 169
Biological sequences	p. 171
Encoding genomes	p. 172
Matching patterns	p. 173
Matching single query sequences	p. 174
Matching many query sequences	p. 175
Palindromes and paired matches	p. 177
Alignments	p. 179
Foreign Language Interfaces	p. 183
Introduction	p. 183
Overview	p. 184
The C programming language	p. 185
Calling C and FORTRAN from R	p. 185
.C and .Fortran	p. 186
Using .Call and .External	p. 187
Writing C code to interface with R	p. 188
Registering routines	p. 188
Dealing with special values	p. 189
Single precision	p. 191
Matrices and arrays	p. 191
Allowing interrupts	p. 193
Error handling	p. 193
R internals	p. 193
S4 OOP in C	p. 197
Calling R from C	p. 198
Using the R API	p. 198
Header files	p. 198
Sorting	p. 199
Random numbers	p. 199
Loading libraries	p. 202
Inspecting DLLs	p. 203
Advanced topics	p. 204
External references and finalizers	p. 204
Evaluating R expressions from C	p. 206
Other languages	p. 209
R Packages	p. 211
Package basics	p. 212
The search path	p. 212
Package information	p. 213
Data and demos	p. 215
Vignettes	p. 215
Package management	p. 216
biocViews	p. 218
Managing libraries	p. 219
Package authoring	p. 219
The DESCRIPTION file	p. 220
R code	p. 220
Documentation	p. 221
Name spaces	p. 224
Finding out about name spaces	p. 226
Initialization	p. 226
Event hooks	p. 227
Data Technologies	p. 229
Introduction	p. 229
A brief description of GO	p. 229
Using R for data manipulation	p. 230
Aggregation and creating tables	p. 230
Apply functions	p. 232
Efficient apply-like functions	p. 234
Combining and reshaping rectangular data	p. 234
Example	p. 236
Database technologies	p. 238
DBI	p. 239
SQLite	p. 241
Using AnnotationDbi	p. 243
XML	p. 254
Simple XPath	p. 256
The XML package	p. 257
Handlers	p. 257
Example data	p. 258
DOM parsing	p. 258
XML event parsing	p. 261
Parsing HTML	p. 263
Bioinformatic resources on the WWW	p. 264
PubMed	p. 265
NCBI	p. 265
biomaRt	p. 266
Getting data from GEO	p. 270
KEGG	p. 272
Debugging and Profiling	p. 273
Introduction	p. 273
The browser function	p. 274
A sample browser session	p. 275
Debugging in R	p. 276
Runtime debugging	p. 277
Warnings and other exceptions	p. 278
Interactive debugging	p. 279
The debug and undebug functions	p. 281
The trace function	p. 285
Debugging C and other foreign code	p. 289
Profiling R code	p. 290
Timings	p. 292
Managing memory	p. 293
Memory profiling	p. 294
Profiling memory allocation	p. 295
Tracking a single object	p. 298
References	p. 301
Index	p. 305
Table of Contents provided by Ingram. All Rights Reserved.

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