---
title: Analysis parameters
description: The pathway set, scoring mode and coverage thresholds that FRoGS scoring used. FRoGS is deprecated, its backend is offline, and it can no longer be run.
---

These settings control how [frogs](/docs/frogs) scores compounds against pathways — the pathway set, how compound-target links and signatures are weighted, and the coverage and completeness thresholds. The scoring mode and coverage thresholds are what most affect which compounds stay in the analysis and how pathways rank.

> **Not available in chat**

> FRoGS is deprecated on the platform and its Modal backend has been taken offline — it is not registered with the orchestrator, so chat cannot call it. Existing FRoGS job results should be treated as unverified: a still-registered legacy form of the tool faked its results, returning mock predictions as `SUCCESS` regardless of input.

## Core settings

- **Pathway set**: Choose the ontology or custom list to score against.
- **Scoring mode**: Select how compound-target links are weighted (e.g., equal
  weights vs. target-aware weights).
- **Signature weighting**: Optionally weight signatures by quality/confidence if
  your dataset supports it.

## Thresholds

- **Minimum target coverage**: Require a minimum number of mapped targets per
  compound to keep it in the analysis.
- **Signature completeness**: Set a tolerance for missing genes/features;
  signatures below the threshold are dropped with a warning.
- **P-value / FDR cutoffs**: Configure significance thresholds for pathway calls
  when available in your workspace.

## Performance and batching

- Large pathway sets or signature matrices may be batched; keep batch size
  defaults unless you see timeouts.
- If jobs run long, reduce pathway scope or tighten completeness thresholds.

## Recommendations

- Start with the default pathway set and moderate thresholds, then tighten as
  you refine hypotheses.
- Use the same pathway set across related runs to make comparisons consistent.
- When exploring new datasets, enable verbose validation so you can inspect any
  dropped inputs.

 Parameter validation happens server-side. If a submission fails,
the response includes the field name and allowed range to correct the form
quickly.