mergePM {dvir}

Identity and merge matching PM samples

Description

Computes the direct matching LR of each pair of samples, and merges the matching samples.

Usage

mergePM(
  pm,
  threshold = 10000,
  method = c("mostcomplete", "first", "combine"),
  verbose = TRUE
)

Arguments

pm

A list of typed singletons.

threshold

LR threshold for positive identification.

method

A keyword indicating how to merging matching samples. See Details.

verbose

A logical.

Details

The available methods for merging matched samples are:

• "mostcomplete": Use the sample with the highest number of non-missing genotypes

• "first": Use the first in each group, according to the input order

• "combine": Not implemented yet.

Value

A list with the following entries:

• groups: A list containing the groups of matching samples.

• LRmat: A symmetric matrix (with 0s on the diagonal) containing the direct matching LR values.

• nonmissing: A named vector reporting the number of non-missing genotypes for each sample.

• pmReduced: A list of singletons. If use is "best" or "first", this is a subset of the input pm.

See Also

directMatch().

Examples

pm = singletons(c("V1", "V2", "V3")) |> 
  addMarker(V1 = "1/1", V2 = "2/2", V3 = "1/1", 
            afreq = c("1" = 0.01, "2" = 0.99), name = "L1")

mergePM(pm)