os_provenance_preflight.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/singlesample-provenance-preflight.R
\name{os_provenance_preflight}
\alias{os_provenance_preflight}
\title{Single-sample specimen-overlap provenance pre-flight gate}
\usage{
os_provenance_preflight(accessions, manifest_path = NULL)
}
\arguments{
\item{accessions}{Character vector of GEO/ArrayExpress accessions
(e.g., \code{c("GSE211692", "GSE106817")}).}

\item{manifest_path}{Path to a TSV file with columns
\code{acc1, acc2, block_id} (and optionally \code{fraction},
\code{evidence_source}). If \code{NULL}, uses the bundled manifest at
\code{system.file("extdata", "provenance_manifest.tsv", package = "OmicSelector")}.}
}
\value{
List with components:
  \describe{
    \item{\code{status}}{One of \code{"NO_OVERLAP"}, \code{"KNOWN_OVERLAP"},
      \code{"UNKNOWN_ACCESSION"}.}
    \item{\code{overlapping_pairs}}{\code{data.frame} subset of the manifest
      with rows whose \code{acc1} and \code{acc2} are both in the input
      accession list.}
    \item{\code{unknown_accessions}}{Character vector of input accessions
      not present in the manifest.}
    \item{\code{manifest_path}}{Resolved path of the manifest used.}
  }
}
\description{
Audits a candidate accession list against a manifest of known specimen-
overlap pairs and returns one of three exit conditions:
\describe{
  \item{\code{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.}
  \item{\code{KNOWN_OVERLAP}}{At least one pair of input accessions is
    listed in the manifest. The cross-cohort analysis must apply
    block-aware multiplicity correction (\code{\link{singlesample_bh_fdr_correct_blocked}}).}
  \item{\code{UNKNOWN_ACCESSION}}{At least one input accession is not in
    the manifest. Audit required before combining with anything else.
    Takes precedence over \code{KNOWN_OVERLAP}.}
}

Intended as the first stage in the single-sample pipeline (Methods section
"Provenance auditing and specimen-overlap handling").
}
\examples{
res <- os_provenance_preflight(c("GSE211692", "GSE106817"))
res$status

}