Remove automatically generated IDs from pedigree

Identifies automatically generated IDs via isGeneratedUnknownId(), the shared detection predicate derived from the configurable auto-ID format (see getAutoIdFormat). With the default "U%04d", an automatically generated ID is a capital "U" followed by at least four capital letters or digits ("U0001", or "U05X3C" after de-identification). A real animal whose ID merely starts with "U" ("U1", "U123", "Uma") is kept, and so is its place as a sire or dam; a real ID of the full shape ("U1234") is removed unless the pedigree's placeholder column (see qcStudbook) marks it FALSE, and a TRUE mark removes a stand-in whatever its ID looks like. The "four or more" match is a prefix, so an ID such as "U1234abc" is removed too. Sire and dam entries that are generated IDs are set to NA.

Usage

removeAutoGenIds(ped)

Arguments

ped

datatable that is the Pedigree. It contains pedigree information. The fields id, sire and dam are required.

Value

A pedigree with automatically generated IDs removed.

Examples

examplePedigree <- nprcgenekeepr::examplePedigree
length(examplePedigree$id)
#> [1] 3694
ped <- removeAutoGenIds(examplePedigree)
length(ped$id)
#> [1] 2322