How to automate data analysis with R scripts: Scripting for reproducibility (CC027)
Channel: Riffomonas Project
Date: 2020-08-20

In this screencast tutorial, Pat Schloss shows how you can convert an R script into an executable to help automated your data analyses. Along the way he'll revisit previous R commands like read_tsv, rename, pivot_longer, select, filter, and write_table. He'll also show how to integrate these scripts into our bash-based workflow that uses Makefiles. The script he generates converts a very wide count_table file from mothur to a three column wide, tidy data frame, which will be much easier to work with in R. This is an important step in inter- and intra-genomic variation limit the interpretation of amplicon sequence variants (ASVs; aka exact sequence variants or ESVs) for different regions within the 16S rRNA gene. This is an important question for microbiome researchers.

Pat demonstrates these concepts by live coding at the command line interface using RStudio, GitHub Flow, and make. He then turns viewers loose to work through several activities to answer related questions and finishes by giving his solutions.

The accompanying blog post contains the exercises and solutions can be found at http://www.riffomonas.org/code_club/2020-08-20-R-scripts.



Big Swing Band by Audionautix is licensed under a Creative Commons Attribution license (https://creativecommons.org/licenses/by/4.0/)
Artist: http://audionautix.com/