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Normalised Chromosome Value (NCV) score

nipter_ncv_score.Rd

Computes the NCV score for a test sample. The NCV method selects an optimal set of denominator chromosomes that minimises the coefficient of variation (CV) in the control group, then uses the resulting ratio to Z-score the test sample.

Usage

nipter_ncv_score(
  sample,
  control_group,
  chromo_focus,
  max_elements = 5L,
  exclude_chromosomes = c(13L, 18L, 21L),
  include_chromosomes = NULL
)

Arguments

sample

A NIPTeRSample object.

control_group

A NIPTeRControlGroup object.

chromo_focus

Integer; the target chromosome (1-22).

max_elements

Maximum number of denominator chromosomes to try (default 5). The algorithm searches all combinations of 1 to max_elements from the candidate pool.

exclude_chromosomes

Integer vector of chromosomes to exclude from the denominator pool (default c(13, 18, 21) — the trisomy chromosomes).

include_chromosomes

Integer vector of chromosomes to force-include in the candidate pool. Default NULL.

Value

A list of class "NIPTeRNCV" with elements:

sample_score

The NCV score for the test sample (numeric).

focus_chromosome

Character; the tested chromosome.

denominators

Integer vector of selected denominator chromosomes.

control_statistics

Named numeric vector with mean, sd, and shapiro_p_value.

control_z_scores

Named numeric vector of control NCV scores.

best_cv

The minimum CV achieved.

correction_status

Character vector.

sample_name

Character.

Details

The candidate denominator pool is: chromosomes 1-12, 14-17, 19-20, 22 (the "control chromosomes") minus exclude_chromosomes minus chromo_focus, plus any include_chromosomes.

For each combination size from 1 to max_elements, all choose(n_candidates, size) combinations are evaluated. The ratio reads[focus] / sum(reads[denominators]) is computed per control sample, and the combination minimising the coefficient of variation (sd/mean) is selected.

See also

nipter_z_score(), nipter_as_control_group()

Examples

if (FALSE) { # \dontrun{
ncv21 <- nipter_ncv_score(sample, cg, chromo_focus = 21, max_elements = 5)
ncv21$sample_score
ncv21$denominators
} # }