Adjust CN labelling ratio and optionally reconstruct CN hits — TRACE_CN_labelling_ratio

This function calculates the labelling ratio of each CN hit across the 4 TRACE sample groups, stores the evaluated group-level ratio in `object@advancedAna$TRACE_temp$cn.group.ratio` and per-seed ratios in `object@advancedAna$TRACE_temp$cn.ratio.df`, and optionally reconstructs the CN hit network by re-running `TRACE_get_CN_net()` with the new `ratio.adjust`.

Usage

TRACE_CN_labelling_ratio_adjust(
  object,
  eval_top = 0.2,
  plot = FALSE,
  reconstruct = TRUE
)

Arguments

object: MSdev object.
eval_top: Proportion in `(0, 1]` used to select top `TRACE_cor` entries for ratio-adjust evaluation.
plot: Logical. If `TRUE`, draw labelling-ratio jitter/crossbar plot for the top `eval_top` `TRACE_cor` entries.
reconstruct: Logical. If `TRUE`, re-run `TRACE_get_CN_net()` using the evaluated 4-group labelling ratio as `ratio.adjust`.

Value

Updated MSdev object.