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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
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Dan MacLean
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Toc

Table of Contents (13) Chapters Close

Preface 1. Performing Quantitative RNAseq 2. Finding Genetic Variants with HTS Data FREE CHAPTER 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 simple S3 objects to simplify code

Creating your own objects can do a great deal to simplify your code and workflows, making them easier for you to reproduce and reuse and abstracting away a lot of the internal logic of a program so that the cognitive load on you as a programmer is reduced and you can concentrate more on the bioinformatic and analytical aspects of the project you're working on. R actually has numerous ways of creating objects and classes. In this recipe, we'll look at its simplest, most ad hoc method—S3. This is a pretty informal way of creating objects and classes but does suffice in a lot of cases.

Getting ready

In this recipe, we'll need just base R functions, so there&apos...

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