Get Sarek CNA output files for a SCOUT SPN — get_sarek_cna • SCOUT

Returns a named list of CNA file paths from the Sarek copy-number calling results for a given sample, coverage, purity and caller.

Usage

get_sarek_cna(
  spn,
  sample_id,
  coverage,
  purity,
  caller,
  normal_id = "normal_sample"
)

Arguments

spn: SPN identifier, e.g. "SPN01".
sample_id: Sample identifier.
coverage: Sequencing coverage (integer).
purity: Sample purity (0–1).
caller: CNA caller: "ascat", "sequenza", or "cnvkit".
normal_id: Normal sample ID. Defaults to "normal_sample".

Value

Named list of file paths (keys depend on caller, e.g. segments, purityploidy, cnvs, etc.).

Examples

if (FALSE) { # \dontrun{
get_sarek_cna("SPN01", "SPN01_1", 100, 0.9, "ascat")
} # }