Interpret a NIPTmer score row into a compact call

Interpret a NIPTmer score row into a compact call

Usage

niptmer_interpret(
  scored_table,
  sample_index = nrow(scored_table),
  default_threshold = 4,
  special_threshold = 3.5,
  special_chromosomes = c("13", "18", "21"),
  distance_cutoffs = c(5, 6.5),
  sex_call_spec = NULL
)

Arguments

scored_table

Output of niptmer_score_samples().

sample_index

One-based row index to interpret (default: last sample).

default_threshold

Absolute z-score threshold for chromosome flags.

special_threshold

Absolute z-score threshold for chromosomes 13, 18, 21.

special_chromosomes

Chromosomes using special_threshold.

distance_cutoffs

Numeric vector of length 2 defining Good, Mid, Bad.

sex_call_spec

Optional named list overriding sex chromosome call thresholds. Defaults preserve current behavior: list(girl = list(euploid_abs = 3, call = 4), boy = list(euploid_abs = 3, call = 3.5)).

Value

A one-row data.frame with SampleName, AA, SA, Distance and Gender.