kinshipMatrixToKValues: Extracts a dataframe with a row for each kinship coeficient...

In rmsharp/nprcmanager: Genetic Tools for Colony Management

Extracts a dataframe with a row for each kinship coeficient in the kinship matrix

Description

A kValue matrix has one row for each pair of individuals in the kinship matrix and one column for each kinship matrix. Thus, in a kinship matrix with 20 individuals the kinship matrix will have 20 rows by 20 columns but only the upper or lower triangle has unique information as the diagonal values are by definition all 1.0 and the upper triangle has the same values as the lower triangle. The kValue table will have 20 + (20 * 19) / 2 elements with the 20 values from the kinship coeficient matrix diagonal and 2*19 elements from one of the two triangles.

Usage

kinshipMatrixToKValues(kinshipMatrix)

Arguments

kinshipMatrix

square kinship matrix. May or may not have named rows and columns.

Details

The kValue matrix for 1 kinship matrix for 20 individuals will have 190 rows and 3 columns. The first two columns are dedicated to the ID pairs and the third column contains the pair's kinship coefficient.

Thus, the number of rows in the kValues matrix from one kinship matrix will be n + \eqn{n(n-1)}{2} and the number of columns will be 3.

Value

data.frame object with columns id_1, id_2, and kinship where the first two columns contain the IDs of the individuals in the kinship matrix provided to the function and the kinship columm contains the corresponding kinship coefficient. In contrast to the kinship matrix. Each possible pairing of IDs appears once.

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)]
}

simPed <- makeSimPed(ped, allSimParents)
simKinship <- kinship(simPed$id, simPed$sire,
                      simPed$dam, simPed$gen)
kValues <- kinshipMatrixToKValues(simKinship)

rmsharp/nprcmanager documentation built on Feb. 2, 2025, 12:45 a.m.