| 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 |
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