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bravo (version 4.1.0)

parameter_selection: Select Optimal Tuning Parameters

Description

Full training step: cleans SNP matrix and tunes SVEN hyperparameters.

Usage

parameter_selection(
  X,
  R2 = 0.5,
  betamax = 1,
  n.cores = max(1, parallel::detectCores() - 1),
  hitsize = "all",
  MAF_threshold = 0.05
)

Value

A list containing the original SNP matrix, cleaned SNP matrix, optimal parameters, MAF threshold, expected hit size, and number of cores used. The list is assigned class "svenetics_trained" for use in downstream functions.

Arguments

X

Raw SNP matrix (dgCMatrix).

R2

Heritability (default 0.5).

betamax

Maximum effect size magnitude (default 1).

n.cores

Number of cores (default: detectCores() - 1).

hitsize

One of "all", "small", "medium", "large" (default "all").

MAF_threshold

MAF cutoff (default 0.05).