R: Phylogenetic Organization of Metagenomic Signals

# Phylogenetic Organization of Metagenomic Signals

## Documentation for package ‘POMS’ version 1.0.1

- DESCRIPTION file
- Package README

## Help Pages

abun_isometric_log_ratios | Compute isometric log ratio based on abundance of feature sets
compute_node_balances | Compute balances at tree nodes.
filter_rare_table_cols | Filters out columns of dataframe based on number of proportion of non-zero cells
genome_content_phylo_regress | Phylogenetic regression of input vector against function presence/absence.
node_taxa | Determine taxa labels of tips on each side of a node
phylolm_summary | Wrapper for running phylogenetic regression with phylolm
POMS_pipeline | Main function to run POMS pipeline
prep_func_node_info | Get node indices of FSN and BSN categories across tree for a given function
prevalence_norm_logit | Compute additive smoothed prevalence of features (e.g, taxa), restricted to samples of a particular metadata category.
specificity_scores | Compute shrunken specificity score of a feature, which represents how the presence of a feature is associated with a given sample grouping.
subset_by_col_and_filt | Subset dataframe by column names and then post-filter