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CNV Profile Task Example

This tutorial shows how to run the cnv_profile evaluation task. It uses HCC-2T as the example dataset.

Data Source And Assumptions

The HCC example is based on data from GSA-Human accession HRA000437. In practice, raw FASTQ files are first processed with our standard upstream data workflow, and the resulting ST-CNVBench-ready inputs are then used for prep, run, and eval.

In this tutorial, we assume:

  • your data.yaml contains one dataset entry with dataset_id: HCC-2T
  • the standardized input package is already available for that dataset
  • your models.yaml already configures all CNV inference methods included in this benchmark
  • your eval.yaml follows the same parameter structure as configs/templates/eval.template.yaml

For detailed config requirements, see Dataset Preparation, Model Run, and Evaluation.

Step 1: Prepare Data

Run:

st-cnvbench --steps prep \
  --data-config data.yaml \
  --prep-ids HCC-2T

Check the prepared dataset under:

<output.root>/

Expected standardized outputs include:

  • filtered_feature_bc_matrix/
  • filtered_feature_bc_matrix.h5ad
  • spatial/tissue_positions.csv
  • spatial/scalefactors_json.json

Step 2: Run Models

Run all CNV inference methods configured for the benchmark:

st-cnvbench --steps run \
  --data-config data.yaml \
  --model-config models.yaml \
  --prep-ids HCC-2T \
  --exec-mode conda

Check raw model outputs under:

<results_dir>/HCC-2T/<model_name>/

Step 3: Evaluate CNV Profile

Run cnv_profile evaluation across all configured methods:

st-cnvbench --steps eval \
  --data-config data.yaml \
  --eval-config eval.yaml \
  --prep-ids HCC-2T \
  --eval-tasks cnv_profile

Check evaluation outputs under:

<eval_dir>/HCC-2T/cnv_profile/

Typical outputs include:

  • CNV profile metrics summary tables
  • per-method CNV profile comparison plots
  • karyogram-level comparison plots

Example Results

Copy Number Karyogram

This figure shows the copy-number profile karyogram across all methods.

Copy number karyogram across methods

LOH Karyogram

This figure shows the LOH-status karyogram across all methods.

LOH karyogram across methods

PCC Summary

This figure summarizes CNV-profile concordance using the Pearson correlation coefficient.

PCC summary across methods

Max Macro F1 Summary

This figure summarizes discrete CNV-event agreement using the maximum macro F1 score.

Max macro F1 summary across methods

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