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Test 08 - Age of Flagged Analysis

Purpose

Generate age and temporal analyses for flagged cases/controls across specified cohorts. Produces graphs and statistics for cases and controls stratified by cohorts defined in the COHORTS environment variable.

Required Inputs

From configs/env.sh and the test invocation environment:

  • WORK_DIR: Working folder where outputs will be written
  • FIRST_WORK_DIR: Reference run (contains rep and bootstrap JSON)
  • COHORTS: A pipe-separated list of cohort definitions; each item should be name=features where features is a filter string understood by FilterSamples/bootstrap
  • Optional: ALT_PREDS_PATH for comparator comparisons

How to Run

From your TestKit folder, execute:

1
./run.specific.sh 8

Or include as part of the full suite:

1
./run.sh

Outputs are stored under ${WORK_DIR}/age_of_flagged.

What This Test Does

  • If ALT_PREDS_PATH is not set, prints a message noting comparator comparisons will be skipped.
  • For each cohort listed in COHORTS:
    • Uses FilterSamples to create cohort-specific prediction files ${WORK_DIR}/bootstrap/<cohort_name>.preds if not present.
    • Invokes age_of_flagged.py (a Python helper) to compute and plot age distributions and other temporal statistics for the given cohort; outputs go under ${WORK_DIR}/age_of_flagged.

Output Location

  • Per-cohort age analysis: ${WORK_DIR}/age_of_flagged (HTML or image outputs and supporting data files)
  • Per-cohort prediction files used as input: ${WORK_DIR}/bootstrap/<cohort>.preds

How to Interpret Results

  • Open the plots in ${WORK_DIR}/age_of_flagged to inspect age distributions among flagged (predicted high-risk) patients and controls.
  • Compare cohort-specific plots to check consistency (e.g., older average age in one cohort may indicate selection bias).

Common failure modes and suggestions

  • Misformatted COHORTS variable:
    • Ensure COHORTS contains entries like cohortName=featureFilter separated by |.
  • Missing FilterSamples or age_of_flagged.py helper scripts:
    • Ensure the referenced helpers are available under ${CURR_PT}/resources or on PATH.
  • Missing input predictions or samples:
    • Confirm ${WORK_DIR}/bootstrap/eligible_only.preds exists and prediction files referenced by ${FIRST_WORK_DIR} are present.

Test Results Review

Primary files to inspect after running this test:

  • ${WORK_DIR}/age_of_flagged/* (per-cohort graphs)