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license: cc-by-4.0
tags:
- genomics
- chromatin-accessibility
- chorus
- background-distributions
---
# Chorus background CDFs for Cherimoya / CATv1
Per-track background distributions that let [chorus](https://github.com/pinellolab/chorus)
turn a raw Cherimoya prediction into an **effect percentile** and an
**activity percentile**, rather than an uncalibrated fold-change.
This is a staging copy so that
[pinellolab/chorus#107](https://github.com/pinellolab/chorus/pull/107) is
testable before merge. Chorus reads backgrounds from
`lucapinello/chorus-backgrounds` (hardcoded in
`chorus/analysis/normalization.py`), where the other seven oracles' files
live; the intent is for this file to be mirrored or moved there.
| file | tracks | size |
|---|---|---|
| `cherimoya_pertrack.npz` | 1,518 | 154 MiB |
## What's in it
Three sorted 10,000-point empirical CDFs per track, keyed by `ASSAY:ENCSR`
(e.g. `DNASE:ENCSR000EOT` — the ENCODE experiment accession, because
`(assay, biosample)` is ambiguous for 1,188 of the 1,518 CATv1 experiments):
| CDF | built from | supports |
|---|---|---|
| `effect` | 18,672 SNPs — 9,609 random + 9,063 DHS-proximal; `\|log2 FC\|` of alt vs ref over a 501 bp window centred on the variant | effect percentile |
| `summary` | 34,004 baseline positions — random + ENCODE cCREs + protein-coding TSS + Meuleman DHS summits; 501 bp window sum of the reference prediction | activity percentile |
| `perbin` | 32 sampled bins at each of those baselines | per-bin activity axis for the browser |
`signed_flags` is False throughout: DNase/ATAC accessibility is unsigned, so
what matters is effect magnitude.
## Provenance
Every array is accompanied by a `build_config` JSON blob recording the
sampling configuration, fold, device and `cherimoya` version, so a CDF file
can always be traced back to how it was made.
- **Built by** `scripts/build_backgrounds_cherimoya.py` in the PR above
- **Models** [`programmable-genomics/CATv1`](https://huggingface.co/programmable-genomics/CATv1), fold 0
- **Genome** GRCh38
- **Sampling** the shared, seeded variant and region sets in
`chorus/utils/annotations.py`, reproducing the sample counts of the
published `chrombpnet_pertrack.npz` exactly (`effect_counts=18672`,
`summary_counts=34004`) — that match is the check that the sets really are
shared, so Cherimoya's percentiles are comparable to the other oracles'
- **Compute** 1,518 tracks in 11.1 min across 8× H200
## Notes
Fold 0 only, matching chorus' ChromBPNet oracle and the fold its CDFs were
built at. CATv1 uses the same chromosome partition as the ENCODE ChromBPNet
annotations, so fold-0-to-fold-0 comparisons are exact.
The `summary` and `perbin` CDFs contain a small number of slightly negative
values (195 of 15.18M, at most 5 of 10,000 points in any track, minimum
−0.38 counts), always at the extreme low tail. Cherimoya's count head
predicts `log(count + 1)`, so a near-zero-activity window can yield a
slightly negative count under `expm1`. These are left unclamped so that the
builder and `oracle.predict()` compute values identically — that agreement
is what makes a percentile meaningful. The `effect` CDF has no negatives.
## Citation
Cherimoya / CATv1: https://github.com/jmschrei/cherimoya
Chorus: https://github.com/pinellolab/chorus
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