linkage-disequilibrium

R functions to visualize LD measured as the squared correlation coefficient between genotypes (r²).

r2Decay.R

• calculates the r² between pairs of markers separated by increasing genetic distance (up to 1 Mb).
• fits a self-starting non-linear decay function to the average of each bin of marker pairs
• plot this decay function on a log-scale, along with intercepts with the lines y=0.1 and y=0.2

r2HeatMap.R

• plots the r² values between all pairs of markers on a selected chromosome
• VCF files should be thinned prior to plotting (example is thinned to 1 marker / 1 kb)

r2SlidingWindow.R

• calculates the average r² between a given marker, and the next nearest 100 SNPs
• plots the resulting r² values as a Manhattan plot