BLUE_estimates_QT: BLUE_estimates_QT function

In iPRSue: Individual Polygenic Risk Score Uncertainty Estimation

BLUE_estimates_QT function

Description

Estimates individual-level polygenic risk scores (PRS) with uncertainty using a frequentist approach for quantitative traits. This implementation fits a multiple linear regression model in the discovery dataset, computes the coefficient covariance matrix, and applies the delta method to propagate uncertainty to the target dataset.

Usage

BLUE_estimates_QT(
  discovery_pheno,
  discovery_geno_mat,
  target_pheno,
  target_geno_mat,
  significance_level = 0.05
)

Arguments

discovery_pheno	Character. Path to the phenotype file for the discovery dataset. Assumes no header and that the quantitative trait is in the third column.
discovery_geno_mat	Character. Path to the genotype matrix file for the discovery dataset. Assumes no header.
target_pheno	Character. Path to the phenotype file for the target dataset. Assumes no header and individual IDs in the second column.
target_geno_mat	Character. Path to the genotype matrix file for the target dataset. Assumes no header.
significance_level	Numeric. Significance level for confidence intervals (e.g., 0.05 for 95% CI). Default is 0.05.

Details

The function fits a multiple linear regression model (lm) using the discovery data. The estimated SNP effects and their covariance matrix are used to compute PRS and associated uncertainty for each individual in the target dataset. Confidence intervals are constructed using the normal approximation.

Missing or non-estimable coefficients and variances are set to zero.

Value

A data frame with the following columns:

IID

Individual identifier (from the target phenotype file).

PRS

Estimated polygenic risk score for each individual.

Variance

Estimated variance of the PRS.

Lower_Limit

Lower bound of the confidence interval.

Upper_Limit

Upper bound of the confidence interval.

Examples

  qpd <- system.file("Qpd.txt", package = "iPRSue", mustWork = TRUE)
  qpt <- system.file("Qpt.txt", package = "iPRSue", mustWork = TRUE)
  gd  <- system.file("Gd.txt",  package = "iPRSue", mustWork = TRUE)
  gt  <- system.file("Gt.txt",  package = "iPRSue", mustWork = TRUE)
 
  results <- BLUE_estimates_QT(
    discovery_pheno    = qpd,
    discovery_geno_mat = gd,
    target_pheno       = qpt,
    target_geno_mat    = gt,
    significance_level = 0.05
  )
  head(results)

iPRSue documentation built on Sept. 10, 2025, 10:39 a.m.