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

In rmsharp/nprcmanager: Genetic Tools for Colony Management

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

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

rmsharp/nprcmanager documentation built on April 24, 2021, 3:13 p.m.