create_gcae_input_files_2: Create setting 2 for GCAE

In richelbilderbeek/gcaer: Interface to GCAE

Create setting 2 for GCAE

Description

• Date: 2022-03-07

• Goal: assess how well GCAE can predict a phenotype, where the genotype is a simple relationship between the first SNP only and the phenotype

• Hypothesis: it does not matter how many noisy SNPs there are, prediction is always good. Performance decreases with more noise SNPs

• n = 1000

Usage

create_gcae_input_files_2(
  base_input_filename = "setting_2",
  n_individuals = 1000,
  n_random_snps = 0,
  plink_options = plinkr::create_plink_options()
)

Arguments

base_input_filename	base filename of the files to be created
n_individuals	number of individuals
n_random_snps	the number of SNPs that do nothing
plink_options	PLINK options, as created by create_plink_options

Value

a gcae_input_filenames, as can be checked by check_gcae_input_filenames

Author(s)

Richèl J.C. Bilderbeek

Examples

if (plinkr::is_plink_installed()) {
  # Create the files
  gcae_input_filenames <- create_gcae_input_files_2(
    base_input_filename = get_gcaer_tempfilename()
  )

  # Clean up
  file.remove(as.character(unlist(gcae_input_filenames)))
}

richelbilderbeek/gcaer documentation built on March 25, 2024, 3:08 p.m.