Diagnose a NIPTeR control group

Computes per-chromosome Z-scores across all samples in a control group and flags outliers (|Z| > 3). The Shapiro-Wilk test is applied to each chromosome's fraction distribution.

Usage

nipter_diagnose_control_group(control_group)

Arguments

control_group

A NIPTeRControlGroup object.

Value

A list with three elements:

z_scores

Chromosome-by-sample matrix of Z-scores (rows = chromosomes 1-22, columns = samples).

aberrant_scores

A data.frame with columns chromosome, sample_name, z_score for all |Z| > 3, or NULL if none.

statistics

A matrix with rows per chromosome and columns mean, SD, shapiro_p_value.

See also

nipter_as_control_group()

Examples

if (FALSE) { # \dontrun{
diag <- nipter_diagnose_control_group(cg)
diag$aberrant_scores
} # }