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Convert heritability from observed scale to liability scale
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#K=pop prevalence | |
#P=proportion of cases in study | |
#hsq=Heritability estimate (on observed scale) | |
#bigT = liability threshold | |
#tau = density of gaussian | |
K=0.0659 | |
P=0.0659 | |
h2=0.0365 | |
zv <- dnorm(qnorm(K)) | |
h2_liab <- h2 * K^2 * ( 1 - K)^2 / P / (1-P) / zv^2 | |
h2_liab |
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args <- commandArgs(trailingOnly = TRUE) | |
h2 <- args[1] #Observed scale h2 | |
seh2 <- args[2] # SE of h2 | |
pop_prev <- args[3] #population prevalence | |
sample_prev <- args[4] #Sample prevalence (optional) | |
pheno_file <- args[5] #Phenotype (optional) | |
h2 <- as.numeric(h2) | |
seh2 <- as.numeric(seh2) | |
pop_prev <- as.numeric(pop_prev) | |
#If sample prevalence is given | |
if(sample_prev != "xxxx") | |
{ | |
sample_prev <- as.numeric(sample_prev) | |
} | |
#If there is a phenotype file supplied, assume that it has a header and that col 3 is the phenotype, coded as 1= control, 2= case | |
if(pheno_file != "xxxx") | |
{ | |
pheno <- read.table(pheno_file,header=T,stringsAsFactors=F) | |
sample_prev <- length(which(pheno[,3] == 2)) / length(which(pheno[,3] %in% c(1,2))) | |
} | |
#From equation 23 of https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059431/ Estimating Missing Heritability for Disease from Genome-wide Association Studies | |
K <- pop_prev | |
P <- sample_prev | |
zv <- dnorm(qnorm(K)) | |
h2_liab <- h2 * K^2 * ( 1 - K)^2 / P / (1-P) / zv^2 | |
var_h2_liab <- ( seh2 * K^2 * ( 1 - K)^2 / P / (1-P) / zv^2) ^2 | |
p_liab <- pchisq(h2_liab^2/var_h2_liab,1,lower.tail=F) | |
print(c(h2_liab,sqrt(var_h2_liab),p_liab)) |
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