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Compute the full pairwise SSD matrix for a control group

nipter_match_matrix.Rd

Returns the symmetric N×N matrix of sum-of-squared-differences between all pairs of control samples' chromosomal fractions. The diagonal is zero. Row means of this matrix are the per-sample "matching score" used for QC in the production matching loop (see Details).

Usage

nipter_match_matrix(
  control_group,
  exclude_chromosomes = c(13L, 18L, 21L),
  include_chromosomes = NULL,
  cpus = 1L
)

Arguments

control_group

A NIPTeRControlGroup object.

exclude_chromosomes

Integer vector of chromosomes to exclude from the distance calculation (default c(13, 18, 21)).

include_chromosomes

Integer vector of chromosomes to include. If NULL (default), uses all autosomal chromosomes minus exclude_chromosomes.

cpus

Integer; OpenMP threads. Default 1L.

Value

A numeric N×N matrix with sample names as row and column names.

Details

The production NIPT pipeline uses this matrix to identify outlier controls before scoring: each sample's mean SSD against all others is computed, and samples with mean SSD more than 3 SD above the group mean are iteratively removed. This function replaces the lapply over match_control_group calls in CoverageProjectionSCA_Reports.R with a single vectorized Rcpp kernel.

See also

nipter_match_control_group()