Introduction Usage Parameters Output

Output

Path A output (--simulate false)

k-intersection consensus

Output directory: results/k_intersection/

File Description
k_intersection.xlsx XLSX workbook with one sheet per k (k = 1 to n_tools). Each sheet lists taxa called DA by at least k tools in the same direction.
k_<N>_intersection.csv Individual CSV files for each k value

Columns in each sheet/CSV:

  • taxon — taxon identifier
  • direction — majority direction (up or down)
  • n_tools — number of tools calling this taxon DA
  • tools_up — tools calling this taxon DA in the up direction
  • tools_down — tools calling this taxon DA in the down direction

DA tool results (real)

Output directory: results/da_tools_real/<dataset_id>/

Each enabled DA tool produces a TSV file with per-taxon p-values, adjusted p-values, and log-fold change estimates.

Path B output (--simulate true)

Weighted consensus results

Output directory: results/weighted_consensus/

File Description
weighted_consensus_da_taxa.csv Final list of consensus DA taxa with direction and per-tool details

Columns:

  • taxon — taxon identifier
  • direction — consensus direction (up or down)
  • weighted_score — weighted score across tools
  • tools_up — tools calling this taxon up
  • tools_down — tools calling this taxon down
  • det_<tool> — per-tool detection indicator (1/0)

Scoring results

Output directory: results/da_scoring/

File Description
tool_scores.csv Per-tool weights learned from simulations
optimal_threshold.txt The optimal score threshold
threshold_summary.csv Summary of threshold optimisation
global_performance_tools_threshold.png Performance plot across tools and thresholds
tool_metrics_by_dataset.csv Per-tool, per-simulation-scenario metrics
simulation_analysis.rds Full R object with all scoring results

Simulated data

Output directory: results/simulated_data/

File/Directory Description
rds/*.RDS Simulated phyloseq objects
truth/ Ground-truth DA status per simulation scenario
meta/ Simulation metadata
index.csv Index mapping scenario IDs to simulation parameters

DA tool results (simulated)

Output directory: results/da_tools/<scenario_id>/

Per-tool TSV results for each simulated scenario, used by the scoring step.

DA tool results (real)

Output directory: results/da_tools_real/<dataset_id>/

Same as Path A — per-tool TSV files for the real dataset.

Control extraction

Output directory: results/control_extract/ (only if --input_control was not provided)

File Description
control_phyloseq.RDS Phyloseq object containing only control/healthy samples
On this page