Power calculation

power_calc_blood_pressure.R

# Use this library - it handles linear regression instead of assuming balanced ANOVA
library(pwr)

# Just gonna simulate some data but you can obviously use the actual allele frequencies, effect sizes and phenotypic variances


# Allele frequencies:
nsnp <- 29
p <- runif(nsnp)

# Effect sizes:
eff <- rnorm(nsnp)


# Variance of the SNP effects
snpvar <- 2 * p * (1-p) * eff^2


# Phenotypic variance
# e.g. if all SNPs explain 2% of variance then
totvar <- sum(snpvar) / 0.02


# Variance explained by all SNPs (R^2)
r2_total <- sum(snpvar) / totvar
r2_each_snp <- snpvar / totvar


# Other parameters
samplesize <- 5800
multiple_tests <- 50

# Test for all SNPs
pwr.f2.test(
	u = 1, 
	v = samplesize - 2, 
	f2 = r2_total / (1 - r2_total), 
	sig.level = 0.05 / multiple_tests
)

# Test for each SNP
pwr.f2.test(
	u = 1, 
	v = samplesize - 2, 
	f2 = r2_each_snp / (1 - r2_total), 
	sig.level = 0.05 / multiple_tests
)