Returns the reference signature matrices bundled with the package: human COSMIC v3.6 SBS96 and DBS78 for GRCh37 + GRCh38, and ID83 (the build-agnostic indel set, sourced from GRCh37). The data comes from the Alexandrov-lab BSD-2-Clause mirror (SigProfilerAssignment at a pinned commit) – not from cancer.sanger.ac.uk; see [ms_refdb_manifest()] for the full provenance and license record.
Arguments
- version
NULL (default; the bundled version) or the requested version string. Only the bundled version (`"v3.6"`) resolves; anything else is refused with the available version in the message.
- build
NULL (default; every build of each class) or a single genome build (`"GRCh37"` / `"GRCh38"`). A class with no official set for the requested build but declared `build_independent` (ID83) is served with a message naming the nearest official build, exactly as ARCHITECTURE section 6 prescribes.
Value
A named list of [MsRefDb] objects, one per class/build: `SBS_GRCh37`, `SBS_GRCh38`, `DBS_GRCh37`, `DBS_GRCh38` and `ID` (the build-agnostic indel set). A list (not a single object) because one MsRefDb requires all its matrices to share channel labels. Each object's metadata carries `version` (`"v3.6"`), `class`, `build`, `schema_version` (`"1"`), `sha256` (a summary digest over the member files' manifest digests), `license` (`"BSD-2-Clause"`), `build_independent` and `availability`.
Details
**Governance (fail-closed).** Every call re-verifies the bundle: the manifest `schema_version` is checked against the supported set (a forward-incompatible bundle is refused, never read best-effort), every file's SHA-256 is recomputed over the exact bytes, and channel/signature labels must match the manifest exactly (order included). An explicit `version` is honored only if it IS the bundled version – anything else is a structured refusal (the on-demand cache is a later unit), so an analysis can never silently run against a different reference than it named (precedence discipline, ARCHITECTURE section 6).
**Naming deviation (documented).** The bundled accessor is `ms_refdb_bundled()` because `ms_refdb()` is already the exported [MsRefDb] constructor.