nprcgenekeepr (version 1.0.5)

convertRelationships: Converts pairwise kinship values to a relationship category descriptor.

Description

Part of Relations

Usage

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

Arguments

kmat

a numeric matrix of pairwise kinship coefficients. Rows and columns should be named with IDs.

ped

the pedigree information in datatable format with required colnames id, sire, and dam.

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.

Examples

# NOT RUN {
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)
ped <- nprcgenekeepr::qcPed
bkmat <- kinship(ped$id, ped$sire, ped$dam, ped$gen,
                 sparse = FALSE)
relBIds <- convertRelationships(bkmat, ped, c("4LFS70", "DD1U77"))
relBIds
# }
# NOT RUN {
# }