create_dominant_trait: Create a trait in which the phenotype is dominant and the...

In richelbilderbeek/plinkr: Interface to PLINK

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

Description

Create a trait in which the phenotype is dominant and the minor allele frequency is known. The phenotype is fully and perfectly determined by the genotype, see calc_dominant_phenotype_values for the exact phenotypic values

Usage

create_dominant_trait(
  mafs = 0.25,
  n_snps = 1,
  phenotype_value_recessive = 10,
  phenotype_value_dominant = 11
)

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
phenotype_value_recessive	phenotypic value for the recessive variant, i.e. that genotype that is homozygous for the rare allele
phenotype_value_dominant	phenotypic value for the dominant variant, i.e. that genotype that has at least one version of the common common allele

Author(s)

Richèl J.C. Bilderbeek

Examples

create_dominant_trait()
create_dominant_trait(maf = 0.01)
create_dominant_trait(n_snps = 1)

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