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R Bioinformatics Cookbook

You're reading from   R Bioinformatics Cookbook Use R and Bioconductor to perform RNAseq, genomics, data visualization, and bioinformatic analysis

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Product type Paperback
Published in Oct 2019
Publisher Packt
ISBN-13 9781789950694
Length 316 pages
Edition 1st Edition
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Authors (2):
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Dr Dan Maclean Dr Dan Maclean
Author Profile Icon Dr Dan Maclean
Dr Dan Maclean
Dan MacLean Dan MacLean
Author Profile Icon Dan MacLean
Dan MacLean
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Toc

Table of Contents (13) Chapters Close

Preface 1. Performing Quantitative RNAseq FREE CHAPTER 2. Finding Genetic Variants with HTS Data 3. Searching Genes and Proteins for Domains and Motifs 4. Phylogenetic Analysis and Visualization 5. Metagenomics 6. Proteomics from Spectrum to Annotation 7. Producing Publication and Web-Ready Visualizations 8. Working with Databases and Remote Data Sources 9. Useful Statistical and Machine Learning Methods 10. Programming with Tidyverse and Bioconductor 11. Building Objects and Packages for Code Reuse 12. Other Books You May Enjoy

Creating structured and formal objects with the S4 system

S4 is a more formal counterpart to S3, particularly in that it has formal class definitions so it can't be used ad hoc but it does work in quite a similar way to S3, so what we've learned already will be generally applicable. In this recipe, we'll quickly run through how to create a class similar to our SimpleGenome object in the first two recipes of this chapter, with the S4 system. Knowing S4 will be advantageous if you wish to write code to extend Bioconductor, as that is written in S4.

Getting ready

Again, we'll just use base R, so nothing to install.

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