r2 and LD value estimation between significant SNPs identified from GWAS

Question

[rthapa]

Hi,

I want to estimate r2 value and LD value among the significant SNPs discovered from GWAS analysis. Could anyone suggest me what R package is the best and what file format is needed? I would appreciate it.

Thanks

Answer 1

[zx8754]

There are many packages that can do that, depends what format your data is.

• Have a look around this Genetics packages list.
• GWASTools from Bioconductor
• Or just calculate it yourself, see Wikipedia page.
• There is also plink for GWAS type of data.

[rthapa]

Thank you for your reply. Finally I could use TASSEL to get r2 value. I wanted to see LD decay using r2 and distance but my plot looks weird. Do you have any idea?

Thanks!