prs_grid: Create a grid of polygenic risk scores with different tuning...

In vincent10kd/polygenic: Efficient and User-friendly P+T Polygenic Risk Score Creation with Summary Statistics

Create a grid of polygenic risk scores with different tuning parameter combinations

Description

Create a full or fractional factorial grid of polygenic risk scores based on a user-specified range of tuning parameter values. Useful to evaluate the influence of various tuning parameters, and for the creation of stacked scores.

Usage

prs_grid(
  variant_data,
  gwas_info,
  binary_outcome = TRUE,
  imp_range = seq(0.8, 1, 0.05),
  pruning_range = seq(0.7, 1, 0.05),
  pval_range = quantile(gwas_info$pvalue, seq(0.1, 1, 0.1)),
  optimal = FALSE,
  optimal_trials = 9
)

Arguments

variant_data	An object of format output by extract_variants().
gwas_info	An object generated by get_trait_variants() or get_pQTLs().
binary_outcome	Set to TRUE for binary traits, and FALSE for continuous outcomes (including pQTLs)
imp_range	A vector of imputation R^2 values.
pruning_range	A vector of LD (R^2) pruning threshold values.
pval_range	A vector of p-value thresholds.
optimal	If TRUE, creates the grid according to a D-optimal fractional factorial design.
optimal_trials	Number of rows in the fractional factorial design matrix.

Value

A list containing the grid design, a list of all results, and a data.frame with all scores. # grid <- prs_grid(MI_variants, MI_gwas)

vincent10kd/polygenic documentation built on Feb. 25, 2024, 10:17 a.m.