R Programming for Bioinformatics: 1st Edition (Hardback) book cover

R Programming for Bioinformatics

1st Edition

By Robert Gentleman

Chapman and Hall/CRC

328 pages | 2 B/W Illus.

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pub: 2008-07-14
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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.

Reviews

"This is a very excellent book. … I think this is actually the best handbook on R programming that is currently available. … the nine chapters provide an indispensable handbook for R programmers, and an excellent textbook for a graduate course in R programming."

Journal of Statistical Software

Table of 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.

About the Series

Chapman & Hall/CRC Computer Science & Data Analysis

Learn more…

Subject Categories

BISAC Subject Codes/Headings:
MAT029000
MATHEMATICS / Probability & Statistics / General
SCI010000
SCIENCE / Biotechnology