## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ---- eval = FALSE------------------------------------------------------------
#  # install development version of package
#  install.packages("devtools")
#  library("devtools")
#  devtools::install_github("ajbass/lit")

## -----------------------------------------------------------------------------
library(lit)
# set seed
set.seed(123)

# generate SNPs and traits
X <- matrix(rbinom(10 * 10, size = 2, prob = 0.25), ncol = 10)
Y <- matrix(rnorm(10 * 4), ncol = 4)

# test for latent genetic interactions
out <- lit(Y, X)
head(out)

## -----------------------------------------------------------------------------
# load genio package
library(genio)

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

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

# apply lit to plink file
out <- lit_plink(Y, file = file, verbose = FALSE)
head(out)

## ---- eval = FALSE------------------------------------------------------------
#  # apply Marginal (SQ/CP) to loaded genotypes
#  out <- marginal(Y, X)
#  
#  # apply Marginal (SQ/CP) to plink file
#  out <- marginal_plink(Y, file = file, verbose = FALSE)