Determine the pedigree number for each ID

One of Pedigree Curation functions

Usage

findPedigreeNumber(id, sire, dam)

Arguments

id

character vector with unique identifier for an individual

sire

character vector with unique identifier for an individual's father (NA if unknown).

dam

character vector with unique identifier for an individual's mother (NA if unknown).

Value

Integer vector indicating the pedigree (family group) number for each id. Ids that are connected through parent-offspring links share the same number; numbering starts at 1. Numbering starts from ids with both parents unknown (NA), so an id that cannot be reached from such an id, for example one whose only parent is absent from id, or one in a cycle, is returned as NA.

Examples

library(nprcgenekeepr)
library(stringi)
ped <- nprcgenekeepr::lacy1989Ped
ped$gen <- NULL
ped$population <- NULL
ped2 <- ped
ped2$id <- stri_c(ped$id, "2")
ped2$sire <- stri_c(ped$sire, "2")
ped2$dam <- stri_c(ped$dam, "2")
ped3 <- ped
ped3$id <- stri_c(ped$id, "3")
ped3$sire <- stri_c(ped$sire, "3")
ped3$dam <- stri_c(ped$dam, "3")
ped <- rbind(ped, ped2)
ped <- rbind(ped, ped3)
ped$pedigree <- findPedigreeNumber(ped$id, ped$sire, ped$dam)
ped$pedigree
#>  [1] 1 1 1 1 1 1 1 2 2 2 2 2 2 2 3 3 3 3 3 3 3