Data and R scripts for comparison of oral microbiome datasets
R/
all_plaque_pca.R: Converts taxonomic analysis results from raw counts to clr and performs PCA and ANOSIM.effect_plot.R: Converts taxonomic analysis results from raw counts to clr and produces effect plot.machine_learning.R: Trains and tests machine learning classifiers.
data/
metadata_all_samples.tsv: Metadata for all samples used in the analysis.tax_lineage_all_samples.tsv: Taxonomic analysis results for all samples.subgingival_conditions.txt: Disease/health metadata for the subgingival plaque samples.tax_lineage_subgingival.tsv: Taxonomic analysis resilts for subgingival plaque samples.subg_ml_with_metadata.csv: Taxonomic analysis results (clr) and metadata for subgingival plaque samples for machine learning task.