gamut_plink: GAMuT

In lit: Latent Interaction Testing for Genome-Wide Studies

GAMuT

Description

The GAMuT function is a kernel-based multivariate association test. Note that our code to process plink files builds from the genio R package.

Usage

gamut_plink(y, file, adjustment = NULL, pop_struct = NULL, verbose = TRUE)

Arguments

y	matrix of traits (n observations by k traits)
file	path to plink files
adjustment	matrix of covariates to adjust traits
pop_struct	matrix of PCs that captures population structure
verbose	If TRUE (default) print progress.

Value

A data frame of p-values where the columns are the cross products/squared residuals and the rows are SNPs.

See Also

lit_plink, marginal_plink

Examples

# set seed
set.seed(123)

# path to plink files
file <- system.file("extdata", 'sample.bed', package = "genio", mustWork = TRUE)

# Generate trait expression
Y <- matrix(rnorm(10*4), ncol = 4)

out <- gamut_plink(Y, file = file)

lit documentation built on Aug. 8, 2025, 6:17 p.m.