Per-sample QC report

Builds the M4 first-version QC table: per-sample mutation burden (total, log10, burden class), mechanism-level artifact sentinels (G>T share as the oxoG sentinel, C>T share as the FFPE deamination sentinel) and, when a fitted exposure matrix is supplied, the share of exposure carried by the 19 COSMIC artifact signatures (SBS27, SBS43, SBS45–60, SBS95). The Degasperi amber/red tiering is not implemented (v1.x); `qc_flag` applies our declared initial-version constants. The returned table carries the P4 provenance checklist as the `ms_qc_provenance` attribute (see [ms_qc_provenance()]).

Usage

ms_qc_report(catalog, signatures = NULL, exposures = NULL)

Arguments

catalog

An [MsCatalog] in the SBS96 channel space.

signatures

Optional signature matrix (m x k, SBS96 labels) — with `exposures`, enables the artifact-share block.

exposures

Optional k x n count-scale exposure matrix matching `signatures` and the catalog's samples.

Value

A data.frame, one row per sample.

References

COSMIC artifact roster: cancer.sanger.ac.uk/cosmic/signatures/SBS (SBS27, SBS43, SBS45–60, SBS95). oxoG sentinel: Costello et al., NAR 2013 (doi:10.1093/nar/gks1443). FFPE sentinel: Guo et al., Nat Commun 2022 (doi:10.1038/s41467-022-32041-5). Design memo: `vignettes/articles/devlog-2026-10-04-M4-02b-qc-memo.qmd` sections 1, 3 and 4.