Filter control-group outliers

Usage

niptmer_filter_controls(
  count_table,
  controls = NULL,
  chromosomes = as.character(seq_len(22L)),
  z_threshold = 3,
  max_outlier_chromosomes = 1,
  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.
chromosomes: Chromosomes to use for diagnostics.
z_threshold: Absolute z-score threshold defining an outlier chromosome.
max_outlier_chromosomes: Maximum allowed outlier chromosomes before a sample is flagged.
extra_columns: Optional additional predictor columns when count_table is a table/path.

Value

Character vector of controls that pass diagnostics.