R programming: calculate LD for a list of SNPs using 1000G

Question

[luanluansun]

Hi,

I have a list of SNPs and now I would like to calculate the LDs within my list based on 1000G data in R. My issue is now when extracting my list of SNPs from the 1000G, there are some conflicts of the format since my list contains only SNP_id and coordinates while the 1000G were in bed format. Does anyone have tried to do it using some tools rather than one by one manually.

Thanks in advance.

[Mo]

@luanluansun put an example data and write the expected output please

Answer 1

[confusedious]

There is a package on Bioconductor called 'snpStats' that might be worth your time. Check that out.