inheritance: Collapsing (or recoding) genotypes into different categories...

In isglobal-brge/SNPassoc: SNPs-Based Whole Genome Association Studies

Collapsing (or recoding) genotypes into different categories (generally two) depending on a given genetic mode of inheritance

Description

codominant function recodifies a variable having genotypes depending on the allelic frequency in descending order.

dominant, recessive, and overdominant functions collapse the three categories of a given SNP into two categories as follows: Let 'AA', 'Aa', and 'aa' be the three genotypes. After determining the most frequent allele (let's suppose that 'A' is the major allele) the functions return a vector with to categories as follows. dominant: 'AA' and 'Aa-aa'; recessive: 'AA-Aa' and 'aa'; overdominant: 'AA-aa' vs 'Aa'.

additive function creates a numerical variable, 1, 2, 3 corresponding to the three genotypes sorted out by descending allelic frequency (this model is referred as log-additive).

Usage

codominant(o)
dominant(o)
recessive(o)
overdominant(o)
additive(o)

Arguments

o	categorical covariate having genotypes

Value

A snp object collapsing genotypes into different categories depending on a given genetic mode of inheritance

Examples

data(SNPs)
dominant(snp(SNPs$snp10001,sep=""))
overdominant(snp(SNPs$snp10001,sep=""))

isglobal-brge/SNPassoc documentation built on May 15, 2023, 8:10 p.m.