Question: How to plot LD-decay plot?

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dadoudou •

**10**wrote:I got a r2 report file by plink. But I wonder how to get a average R2. That is an example.

For Distance 1 of 5000bp, I can calculate the average of R2 of all SNP-pairs in the distance of 5000bp.

But For Distance 2 of 10000bp, should I calculate the average of R2 of all SNP-pairs in the distance of 10000bp (Thus including the data used in Distance 1), or just calculate the average of R2 of all SNP-pairs in the distance between 5001bp and 10000bp? Which is correct?