Convert pairwise kinship values to relationship categories — convertRelationships • nprcgenekeepr

Part of Relations

Usage

convertRelationships(kmat, ped, ids = NULL, updateProgress = NULL)

Arguments

kmat: a numeric matrix of pairwise kinship coefficients. Animal IDs are the row and column names.
ped: datatable that is the Pedigree. It contains pedigree information. The fields id, sire and dam are required.
ids: character vector of IDs or NULL to which the analysis should be restricted. If provided, only relationships between these IDs will be converted to relationships.
updateProgress: function or NULL. If this function is defined, it will be called during each iteration to update a shiny::Progress object.

Value

A dataframe with columns id1, id2, kinship, relation. It is a long-form table of pairwise kinships, with relationship categories included for each pair. IDs that are not in kmat are ignored. One ID gives that animal's own Self row, and no ID in kmat (or an empty ids) gives a table with no rows.

Examples

library(nprcgenekeepr)
ped <- nprcgenekeepr::smallPed
kmat <- kinship(ped$id, ped$sire, ped$dam, ped$gen, sparse = FALSE)
ids <- c("A", "B", "D", "E", "F", "G", "I", "J", "L", "M", "O", "P")
relIds <- convertRelationships(kmat, ped, ids)
rel <- convertRelationships(kmat, ped, updateProgress = function() {})
head(rel)
#>   id1 id2 kinship               relation
#> 1   A   A   0.500                   Self
#> 2   A   B   0.000            No Relation
#> 3   A   C   0.250       Parent-Offspring
#> 4   A   D   0.250       Parent-Offspring
#> 5   A   E   0.000            No Relation
#> 6   A   F   0.125 Grandparent-Grandchild
ped <- nprcgenekeepr::qcPed
bkmat <- kinship(ped$id, ped$sire, ped$dam, ped$gen,
  sparse = FALSE
)
relBIds <- convertRelationships(bkmat, ped, c("4LFS70", "DD1U77"))
relBIds
#>      id1    id2 kinship relation
#> 1 4LFS70 4LFS70 0.50000     Self
#> 2 4LFS70 DD1U77 0.03125    Other
#> 4 DD1U77 DD1U77 0.50000     Self