Execute CBS on WisecondorX results — .exec

Runs circular binary segmentation on log2-ratios using weights, then splits segments spanning large NA gaps and recalculates segmental ratios. Exact port of upstream CBS.R logic.

Usage

.exec_cbs(
  results_r,
  results_w,
  ref_gender,
  alpha,
  binsize,
  seed,
  parallel = TRUE,
  cpus = 1L
)

Arguments

results_r: List of per-chromosome log2-ratio vectors.
results_w: List of per-chromosome weight vectors.
ref_gender: "F" or "M" — determines whether chrY is included.
alpha: CBS breakpoint p-value threshold.
binsize: Reference bin size in bp.
seed: Optional RNG seed.
parallel: Logical; use ParDNAcopy when available (default TRUE). Falls back to DNAcopy::segment() if ParDNAcopy is not installed.
cpus: Integer; number of threads passed to parSegment(). Only used when parallel = TRUE and ParDNAcopy is available.

Value

Data frame with columns chr (integer, 1-based), start (integer, 0-based bin index), end (integer, exclusive bin index), ratio (numeric, weighted mean segment ratio).