Question: R programming: calculate LD for a list of SNPs using 1000G
gravatar for luanluansun
5.3 years ago by
United Kingdom
luanluansun0 wrote:


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. 






snp R • 1.7k views
ADD COMMENTlink modified 5.3 years ago by confusedious420 • written 5.3 years ago by luanluansun0

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

ADD REPLYlink written 5.3 years ago by Mo920
gravatar for confusedious
5.3 years ago by
confusedious420 wrote:

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

ADD COMMENTlink written 5.3 years ago by confusedious420
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