convert_observed_to_liability_scale {LTFHPlus}

Convert the heritability on the observed scale to that on the liability scale

Description

convert_observed_to_liability_scale transforms the heritability on the observed scale to the heritability on the liability scale.

Usage

convert_observed_to_liability_scale(
  obs_h2 = 0.5,
  pop_prev = 0.05,
  prop_cases = 0.5
)

Arguments

obs_h2

A number or numeric vector representing the liability-scale heritability(ies)on the observed scale. Must be non-negative and at most 1. Defaults to 0.5

pop_prev

A number or numeric vector representing the population prevalence(s). All entries must be non-negative and at most one. If it is a vector, it must have the same length as obs_h2. Defaults to 0.05.

prop_cases

Either NULL or a number or a numeric vector representing the proportion of cases in the sample. All entries must be non-negative and at most one. If it is a vector, it must have the same length as obs_h2. Defaults to 0.5.

Details

This function can be used to transform the heritability on the observed scale to that on the liability scale. convert_observed_to_liability_scale uses either Equation 17 (if prop_cases = NULL) or Equation 23 from Sang Hong Lee, Naomi R. Wray, Michael E. Goddard and Peter M. Visscher, "Estimating Missing Heritability for Diseases from Genome-wide Association Studies", The American Journal of Human Genetics, Volume 88, Issue 3, 2011, pp. 294-305, doi:10.1016/j.ajhg.2011.02.002 to transform the heritability on the observed scale to the heritability on the liability scale.

Value

If obs_h2, pop_prev and prop_cases are non-negative numbers that are at most one, the function returns the heritability on the liability scale using Equation 23 from Sang Hong Lee, Naomi R. Wray, Michael E. Goddard and Peter M. Visscher, "Estimating Missing Heritability for Diseases from Genome-wide Association Studies", The American Journal of Human Genetics, Volume 88, Issue 3, 2011, pp. 294-305, doi:10.1016/j.ajhg.2011.02.002. If obs_h2, pop_prev and prop_cases are non-negative numeric vectors where all entries are at most one, the function returns a vector of the same length as obs_h2. Each entry holds to the heritability on the liability scale which was obtained from the corresponding entry in obs_h2 using Equation 23. If obs_h2 and pop_prev are non-negative numbers that are at most one and prop_cases is NULL, the function returns the heritability on the liability scale using Equation 17 from Sang Hong Lee, Naomi R. Wray, Michael E. Goddard and Peter M. Visscher, "Estimating Missing Heritability for Diseases from Genome-wide Association Studies", The American Journal of Human Genetics, Volume 88, Issue 3, 2011, pp. 294-305, doi:10.1016/j.ajhg.2011.02.002. If obs_h2 and pop_prev are non-negative numeric vectors such that all entries are at most one, while prop_cases is NULL, convert_observed_to_liability_scale returns a vector of the same length as obq_h2. Each entry holds to the liability-scale heritability that was obtained from the corresponding entry in obs_h2 using Equation 17.

References

Sang Hong Lee, Naomi R. Wray, Michael E. Goddard, Peter M. Visscher (2011, March). Estimating Missing Heritability for Diseases from Genome-wide Association Studies. In The American Journal of Human Genetics (Vol. 88, Issue 3, pp. 294-305). doi:10.1016/j.ajhg.2011.02.002

Examples

convert_observed_to_liability_scale()
convert_observed_to_liability_scale(prop_cases=NULL)
convert_observed_to_liability_scale(obs_h2 = 0.8, pop_prev = 1/44, 
                                    prop_cases = NULL)
convert_observed_to_liability_scale(obs_h2 = c(0.5,0.8), 
                                    pop_prev = c(0.05, 1/44), 
                                    prop_cases = NULL)