Select best-matching controls for a sample

Ranks control samples by similarity of chromosomal fractions to a test sample. Uses sum-of-squared differences of collapsed chromosomal fractions (chromosomes 1-12, 14-17, 19-20, 22 by default — excluding trisomy chromosomes 13, 18, 21). The distance computation is accelerated by an Rcpp+OpenMP kernel.

Usage

nipter_match_control_group(
  sample,
  control_group,
  n,
  mode = c("subset", "report"),
  exclude_chromosomes = c(13L, 18L, 21L),
  include_chromosomes = NULL,
  cpus = 1L
)

Arguments

sample

A NIPTeRSample object to match against.

control_group

A NIPTeRControlGroup object.

n

Integer; number of best-matching controls to return.

mode

"subset" (default) returns a new NIPTeRControlGroup; "report" returns a named numeric vector of sum-of-squares scores.

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; number of OpenMP threads for the SSD computation. Default 1L.

Value

A NIPTeRControlGroup (if mode = "subset") or a named numeric vector of sum-of-squares distances (if mode = "report").

See also

nipter_as_control_group(), nipter_match_matrix()