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Estimate proportion of variance of liability explained by SNP in general population

Source: R/add_rsq.r
get_r_from_lor.Rd

This uses equation 10 in Lee et al. A Better Coefficient of Determination for Genetic Profile Analysis. Genetic Epidemiology 36: 214–224 (2012) doi:10.1002/gepi.21614 .

Usage

get_r_from_lor(
  lor,
  af,
  ncase,
  ncontrol,
  prevalence,
  model = "logit",
  correction = FALSE
)

Arguments

lor

Vector of Log odds ratio.

af

Vector of allele frequencies.

ncase

Vector of Number of cases.

ncontrol

Vector of Number of controls.

prevalence

Vector of Disease prevalence in the population.

model

Is the effect size estimated from the "logit" (default) or "probit" model.

correction

Scale the estimated r by correction value. The default is FALSE.

Value

Vector of signed r values