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Get Sarek CNA output files for a SCOUT SPN

get_sarek_cna.Rd

Returns a named list of CNA file paths from the Sarek copy-number calling results. Supported callers: "ascat", "battenberg", "sequenza", "cnvkit".

Usage

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

Arguments

spn

SPN identifier, e.g. "SPN04".

sample

Sample identifier, e.g. "SPN04_1.1".

coverage

Sequencing coverage (integer).

purity

Sample purity: 0.9, 0.6, or 0.3.

caller

CNA caller: "ascat", "battenberg", "sequenza", or "cnvkit".

normal_id

Normal sample ID. Defaults to "normal_sample".

Value

Named list of file paths (keys depend on caller).

Examples

if (FALSE) { # \dontrun{
get_sarek_cna("SPN04", "SPN04_1.1", 100, 0.3, "ascat")
get_sarek_cna("SPN04", "SPN04_1.1", 100, 0.3, "battenberg")
get_sarek_cna("SPN04", "SPN04_1.1", 100, 0.3, "sequenza")
} # }