Frequency and Nonlinear Correlation Hybrid Network Inference

Documentation for package ‘Fancy’ version 0.99.4

$-method	Access FancyResult slots with '$'
bootstrap_networks	Bootstrap network inference
clean_sample_names	Clean sample names from TSV column headers
clr_normalize	CLR-normalise a count table
export_cytoscape	Export a fancy result for Cytoscape
fancy	Run the full Fancy hybrid network inference pipeline
FancyResult-class	FancyResult: S4 container for Fancy pipeline output
fancy_tiny_clr	Tiny example CLR-transformed abundance table
fancy_tiny_counts	Tiny example count table
fancy_tiny_coverage	Tiny example covered-fraction table
fancy_tiny_metadata	Tiny example sample metadata
fancy_tiny_taxonomy	Tiny example GTDB taxonomy table
filter_mags	Filter MAGs by coverage and prevalence
find_optimal_k	Find optimal k for the kNN MI estimator
hybrid_score	Compute hybrid edge score
parse_count_tables	Parse per-sample TSV files into combined MAG-by-sample matrices
parse_gtdb_taxonomy	Parse a GTDB-format taxonomy file
phyla_palette	Assign colours to phyla
plot-method	Plot the hybrid score distribution of a FancyResult
plot_k_elbow	Plot elbow curve for k selection
plot_network	Plot the co-abundance network
show-method	Display a FancyResult
threshold_edges	Threshold scored edges