GitHub - elifesciences-publications/mgs-bias-manuscript: Analysis for McLaren, Willis, and Callahan (2019) (original) (raw)
McLaren MR, Willis AD, Callahan BJ. 2019. Consistent and correctable bias in metagenomic sequencing measurements. bioRxiv 559831.https://www.biorxiv.org/content/10.1101/559831v2
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 themetacal 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 withdevtools::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 thedata() 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