Data and analysis for McLaren, Willis, and Callahan (2019)

McLaren MR, Willis AD, Callahan BJ. 2019. Consistent and correctable bias in metagenomic sequencing experiments. eLife 8:46923. DOI: https://doi.org/10.7554/eLife.46923

This repository

This repository contains the code and data for reproducing the analysis in our manuscript. It is structured as an R package, as explained here. To reproduce our analysis, first install the manuscript version of the metacal R package

# install.packages("devtools")
devtools::install_github("mikemc/metacal@v0.1.0-manuscript")

Then, download this package from GitHub or by running

git clone https://github.com/mikemc/mgs-bias-manuscript

You can then knit or run the R-markdown documents in analysis/, which are described below. These documents include code to load this package with devtools::load_all(), so you do not need to install this package itself. Various other R packages are needed to run the code in the analysis/ documents; these are listed in the "Imports" field of the DESCRIPTION file and can be installed all at once with

devtools::install_deps("path/to/mgs-bias-manucript")

Data

The scripts we used to download and/or generate the necessary sample metadata, 16S and metagenomic taxonomic profiles, and taxon information for our analyses are in data-raw/. This folder also contains scripts that clean the data and save it as .rda (R data) objects that can be loaded with the data() function once the R package is loaded; these objects serve as the starting point for subsequent analyses. An explanation of how to use these scripts is given in the directory's Readme file.

Analysis

Analyses are contained in R-markdown documents in analysis/. Versions already rendered to html can be seen at

• Calculations for conceptual examples discussed in the manuscript
• Estimating genome statistics for the Brooks et al (2015) species
• Analysis of the Brooks et al (2015) dataset
• Analysis of the Costea et al (2017) dataset