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About this book
The Bioconductor project was initiated in 2001 to provide a resource of R packages that specifically address bioinformatics problems. Written by the leader of this project and the original developer of the R software, Bioinformatics with R provides an overview of techniques to develop R programming skills for bioinformatics. The book presents comprehensive coverage of a broad range of key topics, including R language fundamentals, object-oriented programming in R, foreign language interfaces, building R packages, handling different data technologies, and debugging. It includes a number of detailed illustrative bioinformatics examples as well as exercises to demonstrate techniques.
Contents
Introducing R Motivation A note on the text R Language Fundamentals Data structures Managing your R session Language basics Subscripting and subsetting Vectorized computations Replacement functions Functional programming Writing functions Flow control Exception handling Evaluation Lexical scope Graphics Object-Oriented Programming in R The basics of OOP S3 OOP S4 OOP Using classes and methods in packages Documentation Debugging Managing S3 and S4 together Navigating the class and method hierarchy Input and Output in R Basic file handling Connections File input and output Source and sink: capturing R output Tools for accessing files on the Internet Working with Character Data Built-in capabilities Regular expressions Prefixes, suffixes and substrings Biological sequences Matching patterns Foreign Language Interfaces Calling C and FORTRAN from R Writing C code to interface with R Using the R API Loading libraries Advanced topics Other languages R Packages Package basics Package management Package authoring Initialization Data Technologies Using R for data manipulation Example Database technologies XML Bioinformatics resources on the WWW Debugging and Profiling The browser function Debugging in R Debugging C and other foreign code Profiling R code Managing memory References An Introduction appears at the beginning of each chapter.
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