Counts the number of occurrences of each kinship value seen for a pair of individuals in a series of simulated pedigrees.

Usage

countKinshipValues(kinshipValues, accummulatedKValueCounts = NULL)

Arguments

kinshipValues: matrix of kinship values from simulated pedigrees where each row represents a pair of individuals in the pedigree and each column represents the vector of kinship values generated in a simulated pedigree.
accummulatedKValueCounts: list object with same structure as that returned by this function.

Value

A list of three lists named kIds (kinship IDs), kValues (kinship values), and kCounts (kinship counts).

Examples

 library(nprcgenekeepr)
 ped <- nprcgenekeepr::smallPed
 simParent_1 <- list(id = "A",
                     sires = c("s1_1", "s1_2", "s1_3"),
                     dams = c("d1_1", "d1_2", "d1_3", "d1_4"))
 simParent_2 <- list(id = "B",
                     sires = c("s1_1", "s1_2", "s1_3"),
                     dams = c("d1_1", "d1_2", "d1_3", "d1_4"))
 simParent_3 <- list(id = "E",
                     sires = c("A", "C", "s1_1"),
                     dams = c("d3_1", "B"))
 simParent_4 <- list(id = "J",
                     sires = c("A", "C", "s1_1"),
                     dams = c("d3_1", "B"))
 simParent_5 <- list(id = "K",
                     sires = c("A", "C", "s1_1"),
                     dams = c("d3_1", "B"))
 simParent_6 <- list(id = "N",
                     sires = c("A", "C", "s1_1"),
                     dams = c("d3_1", "B"))
 allSimParents <- list(simParent_1, simParent_2, simParent_3,
                       simParent_4, simParent_5, simParent_6)

 extractKinship <- function(simKinships, id1, id2, simulation) {
   ids <- dimnames(simKinships[[simulation]])[[1]]
   simKinships[[simulation]][seq_along(ids)[ids == id1],
                             seq_along(ids)[ids == id2]]
 }

 extractKValue <- function(kValue, id1, id2, simulation) {
   kValue[kValue$id_1 ==  id1 & kValue$id_2 == id2,
          paste0("sim_", simulation)]
 }

 n <- 10
 simKinships <- createSimKinships(ped, allSimParents,
                                  pop = ped$id, n = n)
 kValues <- kinshipMatricesToKValues(simKinships)
 extractKValue(kValues, id1 = "A", id2 = "F", simulation = 1:n)
#>  [1] "sim_1"  "sim_2"  "sim_3"  "sim_4"  "sim_5"  "sim_6"  "sim_7"  "sim_8" 
#>  [9] "sim_9"  "sim_10"
 counts <- countKinshipValues(kValues)
 n <- 10
 simKinships <- createSimKinships(ped, allSimParents, pop = ped$id, n = n)
 kValues <- kinshipMatricesToKValues(simKinships)
 extractKValue(kValues, id1 = "A", id2 = "F", simulation = 1:n)
#>  [1] "sim_1"  "sim_2"  "sim_3"  "sim_4"  "sim_5"  "sim_6"  "sim_7"  "sim_8" 
#>  [9] "sim_9"  "sim_10"
 accummulatedCounts <- countKinshipValues(kValues, counts)