Running R scripts from the command line

August 20, 2020 • PD Schloss • 3 min read

Are you ready for some R? To this point, I’ve been showing you how you can process data files in bash using reproducible practices. Now, we’re going to switch tools and start working with data in R. This will move us closer to quantifying how sensitive and specific amplicon sequence variants are for differentiating bacterial populations in microbiome analyses.

Perhaps you already know a little R. If not, I have several tutorials at the website that you can use for free to learn a lot of fundamentals for analyzing microbiome and other types of data. Typically, when people analyze data in R, they enter commands at the prompt in RStudio. This is a bit like how we could run bash commands from the command line interface. It works and is very powerful. But it isn’t automated and isn’t an approach that will play well with a Makefile. In today’s episode of Code Club, I’ll show you how to create an executable R script that can be run without starting, takes input, and uses good reproducible practices. We’ll see how we can integrate this new script with our earlier analysis.

Even if you’re only watching this video to learn more about R and don’t know what a 16S rRNA gene is, I’m sure you’ll get a lot out of today’s video. Please take the time to follow along on your own computer. If you haven’t been following along but would like to, please check out the notes below where you’ll find instructions on catching up, reference notes, and links to supplemental material. You can find my version of the project on GitHub.

Important things to remember


If you haven’t been following along, you can get caught up by doing the following: