Method (formerly known as cILR) to perform enrichment analysis using competitive balances for microbiome relative abundance data.
Manuscript under review at PLoS Computational Biology. Pre-print available on bioRxiv.
There are files with different use cases
*.pbs files are submission files for the HPC Torque system at Dartmouth to run all analysis plans.
run.R is the main interfacing R script for all *.pbs scripts
renv.lock is the lockfile for renv
There are various directories with different use cases
figures: All the generated figures
R: Contains all primary global cILR functions, data processing and plotting scripts
data: Contains all the data sets available for usage in the manuscript
All analyses are ran as projects using the targets package. Each sub-analysis is a mini project nested using the projects feature. For more documentation for using projects with targets, please refer to the corresponding documentation online. More specifically, each project has a name, a workflow instruction file (prefix script_*.R), and a data store. The file targets.yaml contains all information on sub-analyses available. To run each sub analysis, use the run_new.R file in script mode (e.g. RScript run_new.R --project "sim_diffab").