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.
* import and preprocessing of data from various sources
* statistical modeling of differential gene expression
* biological metadata
* application of graphs and graph rendering
* machine learning for clustering and classification problems
* gene set enrichment analysis
Each chapter of this book describes an analysis of real data using hands-on example driven approaches. Short exercises help in the learning process and invite more advanced considerations of key topics. The book is a dynamic document. All the code shown can be executed on a local computer, and readers are able to reproduce every computation, figure, and table.
This volume's coverage is broad and ranges across most of the key capabilities of the Bioconductor project, including importation and preprocessing of high-throughput data from microarray, proteomic, and flow cytometry platforms:
Curation and delivery of biological metadata for use in statistical modeling and interpretation
Statistical analysis of high-throughput data, including machine learning and visualization
Modeling and visualization of graphs and networks
The developers of the software, who are in many cases leading academic researchers, jointly authored chapters. All methods are illustrated with publicly available data, and a major section of the book is devoted to exposition of fully worked case studies.
This book is more than a static collection of descriptive text, figures, and code examples that were run by the authors to produce the text; it is a dynamic document. Code underlying all of the computations that are shown is made available on a companion website, and readers can reproduce every number, figure, and table on their own computers.