graph_based_covariance_construction {LTFHPlus}

Constructing covariance matrix from local family graph

Description

Function that constructs the genetic covariance matrix given a graph around a proband and extracts the threshold information from the graph.

Usage

graph_based_covariance_construction(
  pid,
  cur_proband_id,
  cur_family_graph,
  h2,
  add_ind = TRUE
)

Arguments

pid

Name of column of personal ID

cur_proband_id

id of proband

cur_family_graph

local graph of current proband

h2

liability scale heritability

add_ind

whether to add genetic liability of the proband or not. Defaults to true.

Value

list with two elements. The first element is temp_tbl, which contains the id of the current proband, the family ID and the lower and upper thresholds. The second element, cov, is the covariance matrix of the local graph centered on the current proband.

Examples

fam <- data.frame(
  id = c("pid", "mom", "dad", "pgf"),
  dadcol = c("dad", 0, "pgf", 0),
  momcol = c("mom", 0, 0, 0))

thresholds <- data.frame(
  id = c("pid", "mom", "dad", "pgf"),
  lower = c(-Inf, -Inf, 0.8, 0.7),
  upper = c(0.8, 0.8, 0.8, 0.7))

graph <- prepare_graph(fam, icol = "id", fcol = "dadcol", mcol = "momcol", thresholds = thresholds)

graph_based_covariance_construction(pid = "id",
                                    cur_proband_id = "pid",
                                    cur_family_graph = graph,
                                    h2 = 0.5)