calc_dominant_phenotype_values: Calculate the phenotypic values for a trait that is dominant.

In richelbilderbeek/plinkr: Interface to PLINK

Calculate the phenotypic values for a trait that is dominant.

Description

Calculate the phenotypic values for a trait that is dominant. It is assumed that adenine is the dominant genotype, and the other nucleotides are recessive. Per SNP, if there is at least one adenine, the phenotypic value is phenotype_value_dominant. else the phenotypic value is phenotype_value_recessive.

Usage

calc_dominant_phenotype_values(
  snvs,
  phenotype_value_recessive = 10,
  phenotype_value_dominant = 11
)

Arguments

snvs	a tibble that contains the two nucleotide calls for multiple individuals. Each column is a haplotype, hence, for a diploid organism, there are two columns. Each individual is represented by a row. Nucleotides are in uppercase. Per SNV table, there can be only two different nucleotides, as this is how a SNP works; a SNP from A to C is a different one (and has a different SNP ID) than a SNP that encodes a mutation for A to G. Use create_snvs to create a snvs.
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

Details

If there are more SNPs, the phenotypic values are averaged.

Note

the reason a these phenotypic value are 10.0 and 11.0, instead of -say- 0.0 and 1.0, is due to PLINK: if phenotypic values are all only zeroes and ones (and twos), PLINK will interpret these as case-control codes. There is no way to force PLINK to do a quantitative trait analysis on zeroes and ones.

As a workaround, phenotypic values start from ten.

Author(s)

Richèl J.C. Bilderbeek

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