R Programming for Bioinformatics

Bioinformatics

Robert Gentleman

Programming for

Bioinformatics

R Programming for Bioinformatics

R

Gentleman

From the co-developer of R and lead founder of the Bioconductor project

Due to its data handling and modeling capabilities as well as its exibility, 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 rst-hand experiences as an expert in R, the book

begins with coverage of 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 proling 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.

Features

Covers the fundamentals of the R language and object-oriented •

programming in R

Discusses XML, SOAP, and other data mark-up and web services •

languages and tools

Deals with many of the standard sequence similarity tools that play a •

prominent role in computational biology

Explores the interaction of R with other languages, such as C, FORTRAN, •

Perl, and Python

Explains how to write your own software packages as well as debug and •

prole R code

Contains complete source code on the book’s website •

C6367

C6367_Cover.indd 1 6/12/08 11:52:13 AM