estimate_gen_liability_ltfh {LTFHPlus}

Estimate genetic liability similar to LT-FH

Description

Estimate genetic liability similar to LT-FH

Usage

estimate_gen_liability_ltfh(
  h2,
  phen,
  child_threshold,
  parent_threshold,
  status_col_offspring = "CHILD_STATUS",
  status_col_father = "P1_STATUS",
  status_col_mother = "P2_STATUS",
  status_col_siblings = "SIB_STATUS",
  number_of_siblings_col = "NUM_SIBS",
  tol = 0.01
)

Arguments

h2

Liability scale heritability of the trait being analysed.

phen

tibble or data.frame with status of the genotyped individual, parents and siblings.

child_threshold

single numeric value that is used as threshold for the offspring and siblings.

parent_threshold

single numeric value that is used as threshold for both parents

status_col_offspring

Column name of status for the offspring

status_col_father

Column name of status for the father

status_col_mother

Column name of status for the mother

status_col_siblings

Column name of status for the siblings

number_of_siblings_col

Column name for the number of siblings for a given individual

tol

Convergence criteria of the Gibbs sampler. Default is 0.01, meaning a standard error of the mean below 0.01

Value

Returns the estimated genetic liabilities.

Examples

phen <- data.frame(
CHILD_STATUS = c(0,0),
P1_STATUS = c(1,1),
P2_STATUS = c(0,1),
SIB_STATUS = c(1,0),
NUM_SIBS = c(2,0))

h2 <- 0.5
child_threshold <- 0.7
parent_threshold <- 0.8

estimate_gen_liability_ltfh(h2, phen, child_threshold, parent_threshold)