create_demo_assoc_data: Create a set of 'assoc' parameters to demonstrate PLINKs...

In richelbilderbeek/plinkr: Interface to PLINK

Create a set of assoc parameters to demonstrate PLINKs --assoc functionality

Description

This function creates:

• Individuals that have all combinations of SNPs exactly once, as created by the create_demo_ped_table function

• All SNPs that are on different chromosomes as created by the create_demo_map_table function

• Traits that follow different genotype to phenotype mapping:

  • control: a trait that is random

  • additive: a trait that is perfectly additive, see calc_additive_phenotype_values for the exact calculation

  • epistatic: a trait that is epistatic, see calc_epistatic_phenotype_values for the exact calculation

Usage

create_demo_assoc_data(
  n_individuals = 3,
  trait = create_random_case_control_trait()
)

Arguments

n_individuals	the number of individuals. Use check_n_individuals to check if this is a valid value
trait	one trait with a clear genetic architecture and a known minor allele frequency, as created by create_trait. Use is_one_trait to detect if something is one trait

Note

This function is named after the --assoc PLINK flag.

Author(s)

Richèl J.C. Bilderbeek

Examples

# Default
create_demo_assoc_data()

# Add more individuals
create_demo_assoc_data(n_individuals = 16)

# Use a random trait
create_demo_assoc_data(
  trait = create_random_trait()
)

# Use an additive trait
create_demo_assoc_data(
  trait = create_additive_trait()
)

# Use an epistatic trait
create_demo_assoc_data(
  trait = create_epistatic_trait()
)

richelbilderbeek/plinkr documentation built on March 25, 2024, 3:18 p.m.