Single-sample specimen-overlap provenance pre-flight gate — os_provenance

Audits a candidate accession list against a manifest of known specimen- overlap pairs and returns one of three exit conditions:

NO_OVERLAP: No accession in the input list overlaps with any other accession in the input list according to the manifest, and every supplied accession appears (as either side of a pair) somewhere in the manifest.
KNOWN_OVERLAP: At least one pair of input accessions is listed in the manifest. The cross-cohort analysis must apply block-aware multiplicity correction (singlesample_bh_fdr_correct_blocked).
UNKNOWN_ACCESSION: At least one input accession is not in the manifest. Audit required before combining with anything else. Takes precedence over KNOWN_OVERLAP.

Intended as the first stage in the single-sample pipeline (Methods section "Provenance auditing and specimen-overlap handling").

Usage

os_provenance_preflight(accessions, manifest_path = NULL)

accessions: Character vector of GEO/ArrayExpress accessions (e.g., c("GSE211692", "GSE106817")).
manifest_path: Path to a TSV file with columns acc1, acc2, block_id (and optionally fraction, evidence_source). If NULL, uses the bundled manifest at system.file("extdata", "provenance_manifest.tsv", package = "OmicSelector").

List with components:

status: One of "NO_OVERLAP", "KNOWN_OVERLAP", "UNKNOWN_ACCESSION".
overlapping_pairs: data.frame subset of the manifest with rows whose acc1 and acc2 are both in the input accession list.
unknown_accessions: Character vector of input accessions not present in the manifest.
manifest_path: Resolved path of the manifest used.

res <- os_provenance_preflight(c("GSE211692", "GSE106817"))
res$status
#> [1] "KNOWN_OVERLAP"