Phylogenetic Organization of Metagenomic Signals

Documentation for package ‘POMS’ version 1.0.1

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