create_epistatic_trait: Create a trait in which the phenotype is epistatic and the...

In richelbilderbeek/plinkr: Interface to PLINK

Create a trait in which the phenotype is epistatic and the minor allele frequency is known.

Description

Create a trait in which the phenotype is epistatic (i.e. determined by multiple SNPs) and the minor allele frequency is known.

Usage

create_epistatic_trait(
  mafs = 0.25,
  n_snps = 2,
  regular_phenotype_value = 20,
  epistatic_phenotype_value = 21
)

Arguments

mafs	one or more minor allele frequencies. These allele frequencies must be ordered decreasingly, i.e. the MAF is at the first position, where the even rarer alleles are at the second and third positions. Note that PLINK cannot handle triallelic nor quadallelic SNPs: PLINK will give a warning that it is setting the rarest alleles to missing.
n_snps	the number of SNPs, as can be checked by check_n_snps
regular_phenotype_value	the regular phenotypic value
epistatic_phenotype_value	the phenotypic value when the epistatic phenotype is expressed

Details

The phenotype is fully and perfectly determined by the genotype, see calc_epistatic_phenotype_values for the exact phenotypic values

Author(s)

Richèl J.C. Bilderbeek

Examples

create_epistatic_trait()
create_epistatic_trait(maf = 0.01)
create_epistatic_trait(n_snps = 3)
create_epistatic_trait(regular_phenotype_value = 3.14)
create_epistatic_trait(epistatic_phenotype_value = 2.71)

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