I am now working to create a LD vs distance plot in R using an output from PLINK which contain seven columns:
CHR_A, BP_A, SNP_A, CHR_B, BP_B, SNP_B, R2. Then I subtract the value of BP_B and BP_A, plot it with R2 value. The graph looks nice, however, I want my graph to have an average line like an example of FIGURE5 in here http://www.hutton.ac.uk/webfm_send/546. How can I add in the line, what should be a code in R for that?