I wanted to plot the r2 LD values along chromosomes. I have my table produced with PLINK which has r2 values for each pair of SNPs within 1000 kb windows. One way to do it would be to average the r2 values within each window. But I would like to have the points every 20 kb apart along the chromosome, as I would later run some correlation analysis using these points and other estimates like along chromosome gene density, along chromosome global Fst etc.
So my question is can I average the LD r2 at every 20 kb block inside the 1000 kb windows? Is there any other way to get the LD values along chromosome at every 20 kb apart?
Thanks for any comments and suggestions