Question: How to plot LD-decay plot?
0
gravatar for dadoudou
4.4 years ago by
dadoudou0
Hong Kong
dadoudou0 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?

sequencing snp plink R • 3.4k views
ADD COMMENTlink modified 3.9 years ago by kane0 • written 4.4 years ago by dadoudou0
0
gravatar for Mohammad Ghoreishi
3.9 years ago by
Iran/Karaj/Tehran University
Mohammad Ghoreishi50 wrote:

you should classified your distance based on average intermarker spacing of yoour data. for example:

2kb-5kb

5kb-10k

10kb-15kb

15kb-20kb

...

if you want you can send an email for me. i will attach an excel file aboul ld decay.

goreishi@gmail.com

ADD COMMENTlink written 3.9 years ago by Mohammad Ghoreishi50
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