Compute Match QC score for one sample — niptmer_match

Match QC is the average sum-of-squared differences in chromosomal fractions between one sample and a control set, inspired by the NIPTeR workflow.

Usage

niptmer_match_qc(
  count_table,
  sample,
  controls = NULL,
  exclude_chromosomes = c("13", "18", "21", "X", "Y", "GC"),
  extra_columns = character()
)

Arguments

count_table: A NIPT count table data.frame/file path or a numeric coverage matrix with samples in rows.
sample: Sample identifier (character) or one-based row index.
controls: Optional control sample identifiers or row indices. If NULL, all samples except sample are used.
exclude_chromosomes: Chromosomes excluded from fraction matching. Defaults to c("13", "18", "21", "X", "Y", "GC").
extra_columns: Optional additional predictor columns when count_table is a table/path.

Value

A list with sample id, mean Match QC score and per-control distances.