How to do clustering of SNPs according to linkage disequilibrium (r2) values?

Question

[anikcropscience]

Hello, Hello, I have 1500 SNPs from a genome-wide association mapping (GWAS) that I found significantly associated with a trait of interest. I estimated the linkage disequilibrium (r2) among all possible pairs of 1500 SNPs using PLINK. Now, I want to perform clustering to group the SNPs above an r2 threshold of 0.5. From the PLINK output files, I could generate a triangular matrix in R. But I am not sure how can I perform clustering on that triangle and extract all the SNPs belonging to a cluster above the threshold (0.5) value. Basically, I want to perform clustering and then extract the SNPs from each cluster that contain SNPs with r2 values above the threshold.

Can someone give some suggestions on how to do that in R?

Thank you.

[Raju]

Hello @anikcropscience, have you found a solution for the above question? If yes, please help me with the solution my requirement is also same!!

[anikcropscience]

Hi, no I did not find any solutions for this problem and left it. I did not need to do this in the end. Sorry, for not being helpful in this case.