get_kinship: Construct kinship matrix from graph

In EmilMiP/LTFHPlus: Implementation of LT-FH++

Construct kinship matrix from graph

Description

construct the kinship matrix from a graph representation of a family, centered on an index person (proband).

Usage

get_kinship(fam_graph, h2, index_id = NA, add_ind = TRUE, fix_diag = TRUE)

Arguments

fam_graph	graph.
h2	heritability.
index_id	proband id. Only used in conjuction with add_ind = TRUE.
add_ind	add genetic liability to the kinship matrix. Defaults to true.
fix_diag	Whether to set diagonal to 1 for all entries except for the genetic liability.

Value

A kinship matrix.

Examples

fam <- data.frame(
i = c(1, 2, 3, 4),
f = c(3, 0, 4, 0),
m = c(2, 0, 0, 0)
)

thresholds <- data.frame(
  i = c(1, 2, 3, 4),
  lower = c(-Inf, -Inf, 0.8, 0.7),
  upper = c(0.8, 0.8, 0.8, 0.7)
)

graph <- prepare_graph(fam, icol = "i", fcol = "f", mcol = "m", node_attributes = thresholds)

get_kinship(graph, h2 = 0.5, index_id = "1")
get_kinship(graph, h2 = 1, add_ind = FALSE)

EmilMiP/LTFHPlus documentation built on June 14, 2025, 12:09 p.m.