Testing for significance with microbiome data on individual taxa using R (CC122)
Channel: Riffomonas Project
Date: 2021-07-02

Testing for significance across microbial taxa is a critical tool for analyzing microbiome data. Pat will show how he uses the wilcox.test with tidy data to compare the relative abundance of bacterial taxa (e.g. genus, OTUs, ASVs). After correcting for multiple comparisons using p.adjust, he shows how he would visualize the relative abundance of significant taxa across individuals along with an indicator of the median and intraquartile range.

In this episode, Pat will use data handling functions from the tidyverse including #nest, unnest, map, and #tidy as well as #wilcox.test in RStudio. The accompanying blog post can be found at https://www.riffomonas.org/code_club/2021-07-02-wilcox.test.

If you're interested in taking an upcoming 3 day R workshop, email me at riffomonas@gmail.com!

R: https://r-project.org
RStudio: https://rstudio.com
Raw data: https://github.com/riffomonas/raw_data/releases/latest
Workshops: https://www.mothur.org/wiki/workshops

You can also find complete tutorials for learning R with the tidyverse using...
Microbial ecology data: https://www.riffomonas.org/minimalR/
General data: https://www.riffomonas.org/generalR/

0:00 Introduction
5:19 Testing for significance by SRN status
14:26 Visualizing differences in relative abundance
23:33 Improving appearance of figure
28:35 Recap