calc_epistatic_phenotype_values: Calculate the phenotypic values for a trait that is...

In richelbilderbeek/plinkr: Interface to PLINK

Calculate the phenotypic values for a trait that is epistatic.

Description

Calculate the phenotypic values for a trait that is epistatic.

Usage

calc_epistatic_phenotype_values(
  snvs,
  regular_phenotype_value = 20,
  epistatic_phenotype_value = 21
)

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.
regular_phenotype_value	the regular phenotypic value
epistatic_phenotype_value	the phenotypic value when the epistatic phenotype is expressed

Details

A phenotypic value starts at 20.0. Only genotypes without adenines results in a phenotype of 21.0

Note

the reason a phenotypic value starts at 20.0, instead of 0.0, 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, epistatic traits start from twenty.

Author(s)

Richèl J.C. Bilderbeek

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