Get tumourevo QC result paths — get_tumourevo_qc • SCOUT

Get tumourevo QC result paths

Usage

get_tumourevo_qc(
  spn,
  coverage,
  purity,
  vcf_caller,
  cna_caller,
  tool,
  sample = NULL
)

Arguments

spn: SPN identifier.
coverage: Sequencing coverage (integer).
purity: Sample purity: 0.9, 0.6, or 0.3.
vcf_caller: VCF caller: "mutect2" or "strelka".
cna_caller: CNA caller: "ascat" or "sequenza".
tool: QC tool: "cnaqc", "join_cnaqc", or "tinc".
sample: Sample name. Required for "cnaqc" and "tinc".

Value

Named list of file paths.

Examples

if (FALSE) { # \dontrun{
get_tumourevo_qc("SPN04", 50, 0.6, "mutect2", "sequenza", "cnaqc", "SPN04_1.1")
get_tumourevo_qc("SPN04", 50, 0.6, "mutect2", "sequenza", "join_cnaqc")
} # }