create_gcae_input_files_1: Create setting 1 for GCAE

In richelbilderbeek/gcaer: Interface to GCAE

Create setting 1 for GCAE

Description

• Date: 2022-01-17

• Goal: do the simplest useful simulation possible

• Hypothesis: on the dimensionality reduction plots, there will be three points. With 'points' I really mean points, i.e. not clusters, as there are exactly 3 genotypes

• n = 1000

Usage

create_gcae_input_files_1(
  base_input_filename = "setting_1",
  n_individuals = 1000,
  n_traits = 1,
  n_snps_per_trait = 1,
  plink_options = plinkr::create_plink_options()
)

Arguments

base_input_filename	base filename of the files to be created
n_individuals	number of individuals
n_traits	the number of quantitative traits
n_snps_per_trait	the number of SNPs that determine a trait
plink_options	PLINK options, as created by create_plink_options

Details

Genotype	Phenotype	Allele frequency	Population	Superpopulation
AA	0	25%	A	Americas
AC	50	50%	B	Americas
CC	100	25%	C	Central/South Asia

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_1(
    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.