bcpd / CoordinatedMicrobiome

Analysis for "Neonatal gut and respiratory microbiota: coordinated development through time and space"

CoordinatedMicrobiome

Analysis for Neonatal gut and respiratory microbiota: coordinated development through time and space.

Requires R 3.4.3 and Bioconductor 3.5.

Contents

• CCA.Rmd : Canonical correlation analysis
• metacommunity_post_analysis.Rmd : Further posthoc analysis of CSTs including Generalized additive models
• data/ : OTU tables and metadata
• Composition modeling/ : regression models for each OTU and CST-OTU prediction models
• DMN Cluster Selection/ : Dirichlet Multionomial model search
• SingleIndex/ : R package used to fit single index models

To run

1. Clone this repo
2. From the repo root, run

install("CoordinatedMBDeps", dependencies = TRUE)

This will install all needed dependencies. Caution: this might downgrade your bioconductor installation to version 3.5. Before starting R you may wish to set the environment variable R_LIBS_USER -- or within R .libPaths() -- to an unused directory before proceeding. Or use the bioconductor 3.5 AMI or docker images...

3. rmarkdown::render('Composition Modeling/pairwise_composition_modeling.Rmd')
4. rmarkdown::render('Composition Modeling/get_model_pvals_betas.Rmd') to generate univariate associations for each OTU and CSTs
5. rmarkdown::render('DMN Cluster Selection/normalized_cluster_selection.Rmd') to run DMN resampling procedure
6. rmarkdown::render('CCA.Rmd') for canonical correlation analysis
7. rmarkdown::render('metacommunity_post_analysis.Rmd') for remaining plots

Updates

• Added pseudopackage to collect dependencies
• Removed some obsolete code
• Added some missing data files