Generating Ld Decay Plot!!!

Question

[Aabha]

Dear all in BioStar,

I am working in the field of plant genomics and I want to do whole genome wide association mapping in plant. I have map information according each chromosome and their position, I have selected SSR markers from our genetic linkage map. I have already calculated LD using widely used software “Tassel” and have generated LD plot.

Now I would like generate LD decay plot. As I know to generate LD decay plota pairwise LD values (r2) are plotted against a genetic distance. Now, I am having problem generating LD decay plot.

Here, I would like to hear your advice or experience on generating LD decay plot.

Thanks a lot for your helps in advance.

Best,

[Michael]

Please try to be more specific, what is your problem actually? Is technical with plotting the values you already have, or is it about computation of some values? Pleaase provide an example of the data you have already.

[dodoabdulmajid]

hello i have same problem like you if you found soluton please help me

[Kevin Blighe]

See the comment that I posted, below. It relates to an answer by rmf

Answer 1

[Kevin Blighe]

A good answer posted years later, here: A: LD-decay in a r2 vs distance(cm) plot

Kevin