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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 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

Building Objects and Packages for Code Reuse

In this final chapter, we'll take a look at taking our code out of our own machines and sharing it with the world. The person we'll share with most often will be ourselves! So, with a view to making our own programming lives easier and more streamlined, we'll look at how to create objects and classes to simplify our own workflows and how to bundle them into packages for reuse in other projects. We'll look at tools for sharing code on sites such as GitHub and how to check that everything in your code works the way it is supposed to.

The following recipes will be covered in this chapter:

  • Creating simple S3 objects to simplify code
  • Taking advantage of generic object functions with S3 classes
  • Creating structured and formal objects with the S4 system
  • Simple ways to package code for sharing and reuse
  • Using devtools to...
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