Get started

Install R and packages

All data handling and analyses in this workflow are performed in R. Before you get started,

• Install R and RStudio
• Install and load required packages

TipSource another script

In this workflow, the first script is used to install and load R packages. To make sure that all packages are installed and loaded, one should run that script before every other script. A quick and easy way to do so is to source the script at the beginning of every other script:

# Load packages
source("001_required_packages.R")

Data preparation

Then, to get started with the data analysis, you must first ensure that the raw data is in the right format. Convert raw data into a phyloseq object and save them as .RData files.

For more information about phyloseq, look up McMurdie and Holmes (2013), or their GitHub pages.

• Load auxiliary data (e.g. Excel sheet)
• Construct a phyloseq object from BLAST results
• Save data as .RData

References

McMurdie, Paul J., and Susan Holmes. 2013. “Phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data.” Edited by Michael Watson. PLoS ONE 8 (4): e61217. https://doi.org/10.1371/journal.pone.0061217.