R Programming for Bioinformatics

Description

Due to its data handling and modeling capabilities as well as its flexibility, R is becoming the most widely used software in bioinformatics. R Programming for Bioinformatics explores the programming skills needed to use this software tool for the solution of bioinformatics and computational biology problems.

Drawing on the author’s first-hand experiences as an expert in R, 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.

With numerous examples and exercises, this practical guide focuses on developing R programming skills in order to tackle problems encountered in bioinformatics and computational biology.

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