Recursively collect an individual's ancestors

Part of Pedigree Sampling From PedigreeSampling.R 2016-01-28

Usage

getAncestors(id, ptree)

Arguments

id

character vector of length 1 having the ID of interest

ptree

a list of lists forming a pedigree tree as constructed by createPedTree(ped) where ped is a standard pedigree dataframe.

Value

A character vector of ancestors for an individual ID.

Details

Contains functions to build pedigrees from sub-samples of genotyped individuals.

The goal of sampling is to reduce the number of inbreeding loops in the resulting pedigree, and thus, reduce the amount of time required to perform calculations with SIMWALK2 or similar programs.

An ancestor reached through both parents is returned once for each route. The function stops with an error that names the ids involved when ptree contains a cycle (an animal that is its own ancestor), which is a data error.

A sire or dam that has no entry of its own in ptree is treated as an animal with unknown parents, as qcStudbook() treats it (addParents() adds the entry): it is returned as an ancestor and has no ancestors of its own. The function stops with an error that names the id when id itself is not in ptree.

Examples

library(nprcgenekeepr)
ped <- nprcgenekeepr::qcPed
ped <- qcStudbook(ped, minSireAge = 0, minDamAge = 0)
pedTree <- createPedTree(ped)
pedLoops <- findLoops(pedTree)
ids <- names(pedTree)
allAncestors <- list()

for (i in seq_along(ids)) {
  id <- ids[[i]]
  anc <- getAncestors(id, pedTree)
  allAncestors[[id]] <- anc
}
head(allAncestors)
#> $`0DXI08`
#> character(0)
#> 
#> $`0RZ5LL`
#> character(0)
#> 
#> $`1B71NB`
#> character(0)
#> 
#> $`2FU86J`
#> character(0)
#> 
#> $`2HEFGM`
#> character(0)
#> 
#> $`4LFS70`
#> character(0)
#> 
countOfAncestors <- unlist(lapply(allAncestors, length))
idsWithMostAncestors <-
  names(allAncestors)[countOfAncestors == max(countOfAncestors)]
allAncestors[idsWithMostAncestors]
#> $HLI95R
#>  [1] "WMUJC5" "H00H7D" "ZWBMTP" "HRBVOE" "RD6KMA" "K7QBLH" "UL1ZA5" "VHXHVH"
#>  [9] "NY9FEC" "ZWBMTP" "HRBVOE" "RD6KMA" "TINMGJ" "UKKA3A" "6MXDVM" "AXDMJM"
#> [17] "L6D4ZC" "5EP5AL" "HB9B30" "I31V3S" "3O7TMT" "WORLYK" "FHY041" "43TUN9"
#> [25] "5EP5AL" "HB9B30" "I31V3S" "8G72QV"
#> 
#> $I9TQ0T
#>  [1] "CN4GMN" "QBLTI6" "F0YSEE" "SA1ZC1" "ZXJQQ5" "6MIRJI" "UKK94T" "596J7E"
#>  [9] "82IE3M" "F0YSEE" "SA1ZC1" "ZXJQQ5" "JNWPY2" "MQB1AE" "ZXJQQ5" "BNMWNZ"
#> [17] "DZ3B9K" "CQMWGX" "N2XF08" "P9GZ32" "HKOSVZ" "ZQ0DRX" "RX08B3" "N2XF08"
#> [25] "P9GZ32" "HKOSVZ" "1B71NB" "BRLQFI"
#>