PRS_creator {gnonadd}

Creates poligenic risk scores

Description

This function creates genetic risk scores, with the option of including interactions or dominance effects. The score is automatically shifted to have mean 0.

Usage

PRS_creator(
  g,
  betas,
  dominance_effects = rep(0, length(betas)),
  interaction_effects = matrix(0, nrow = 0, ncol = 0),
  log_scale = FALSE
)

Arguments

g

A matrix, where each colomn represents a variant and each line represents a subject

betas

A numeric vector, representing the (additive) effects of the variants

dominance_effects

A numeric vector, representing dominance effects of the variants

interaction_effects

A matrix with three columns. First two columns are integers that correspond to the variants that are interacting. The third column is the effect size.

log_scale

A Boolian variabe. If true all analysis is done on log-transformed effect values and the resulting score is transformed back to an exponential scale in the end.

Value

A numeric vector with a poligenic risk score for each subject

Examples

g_vec <- matrix(0, nrow = 100000, ncol = 5)
freqs <- runif(ncol(g_vec), min = 0, max = 1)
for(i in 1:ncol(g_vec)){
 g_vec[,i] <- rbinom(100000, 2, freqs[i])
}
beta_vec <- runif(5, min = -0.5, max = 0.5)
dom_vec <- runif(5, min = -0.5, max = 0.5)
int_vec <- matrix(0,nrow = 2, ncol = 3)
int_vec[, 1] <- c(1, 3)
int_vec[, 2] <- c(2, 5)
int_vec[, 3] <- runif(2, min = -0.5, max = 0.5)
res <- PRS_creator(g_vec, beta_vec, dominance_effects = dom_vec, interaction_effects = int_vec)