Summary statistics for imputed kinship values

Makes a data.frame object containing simulated kinship summary statistics using the counts of kinship values list from countKinshipValues.

Usage

summarizeKinshipValues(countedKValues)

Arguments

countedKValues

list object from countKinshipValues function that containes the lists kinshipIds, kinshipValues, and kinshipCounts.

Value

a data.frame with one row of summary statistics for each imputed kinship value. The columns are as follows: id_1, id_2, min, secondQuartile, mean, median, thirdQuartile, max, and sd.

The five-number-summary columns are taken from fivenum: secondQuartile is the lower hinge (fivenum()[2], approximately the first quartile) and thirdQuartile is the upper hinge (fivenum()[4], approximately the third quartile).

Examples

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)
stats <- summarizeKinshipValues(counts)