Analysis for Neonatal gut and respiratory microbiota: coordinated development through time and space.
Requires R 3.4.3 and Bioconductor 3.5.
- 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
- Clone this repo
- 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...
rmarkdown::render('Composition Modeling/pairwise_composition_modeling.Rmd')
rmarkdown::render('Composition Modeling/get_model_pvals_betas.Rmd')
to generate univariate associations for each OTU and CSTsrmarkdown::render('DMN Cluster Selection/normalized_cluster_selection.Rmd')
to run DMN resampling procedurermarkdown::render('CCA.Rmd')
for canonical correlation analysisrmarkdown::render('metacommunity_post_analysis.Rmd')
for remaining plots
- Added pseudopackage to collect dependencies
- Removed some obsolete code
- Added some missing data files