programmable-genomics/chorus-backgrounds

Chorus background CDFs for Cherimoya / CATv1

Per-track background distributions that let 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 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, 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