Estimating and plotting the decay of linkage disequilibrium

A quick post that shows how you can estimate the decay of linkage disequilibrium (LD) and plot it along the genome/chromosome. We’ll be looking at two methods to do this, which unsurprisingly, produce different estimates of LD decay. I personally prefer the 2nd method as it is more scientific.

For both methods, I am using this input file. It basically has two tab delimited columns – one with distance in megabase pairs (Mbp) and the other with LD (r2) values.

First, import the file:

file <- read.table("D_genome_ld.txt", sep="\t", header=T)

1. Method 1: The “Neanderthal” Way (sorry, dear mortal Neanderthals!)

Continue reading