Dcalc: Calculate and visualize LD

In popgenr: Accompaniment to Population Genetics with R: An Introduction for Life Scientists

Description

Calculates the degree of linkage disequilibirum between two biallelic diploid loci and plots the results.

Usage

Dcalc(AABB, AaBB, aaBB, AABb, AaBb, aaBb, AAbb, Aabb, aabb)

Arguments

AABB	Count of A and B double homozygotes.
AaBB	Count of A heterozygotes, B homozygotes.
aaBB	Count of a and B double homozygotes.
AABb	Count of A homozygotes, B heterozygotes.
AaBb	Count of double heterozygotes.
aaBb	Count of a homozygotes, B heterozygote.
AAbb	Count of A and b double homozygotes.
Aabb	Count of A heterozygotes, b homozygotes.
aabb	Count of a and b double homozygotes.

Examples

#assign genotype counts
AABB=2
AaBB=0
aaBB=0
AABb=0
AaBb=1
aaBb=0
AAbb=1
Aabb=0
aabb=0

#run function
Dcalc(AABB, AaBB, aaBB, AABb, AaBb, aaBb, AAbb, Aabb, aabb)

Example output

popgenr documentation built on Feb. 25, 2021, 5:10 p.m.