Estimate Match QC threshold from a control set

Estimate Match QC threshold from a control set

Usage

niptmer_match_qc_threshold(
  count_table,
  controls = NULL,
  exclude_chromosomes = c("13", "18", "21", "X", "Y", "GC"),
  sd_multiplier = 3,
  extra_columns = character()
)

Arguments

count_table

A NIPT count table data.frame/file path or a numeric coverage matrix with samples in rows.

controls

Optional control sample identifiers or row indices. If NULL, all rows are used as controls.

exclude_chromosomes

Chromosomes excluded from fraction matching.

sd_multiplier

Multiplier used for thresholding (mean + k * sd).

extra_columns

Optional additional predictor columns when count_table is a table/path.

Value

A list with control-wise leave-one-out scores and threshold.