How can I interpret linkage analysis result from plink?

Question

[Sharon]

I used the following command to generate linkage analysis, but I can't interpret the results.

plink --file mydata --r2  --ld-window-kb 1000  --ld-window-r2 0.2

Here is the top of the plink.ld file:

 CHR_A         BP_A       SNP_A  CHR_B         BP_B       SNP_B           R2 
     1       752566   rs3094315      1       753541   rs2073813     0.469356 
     1       781258   rs2980314      1       808769  rs12086311            1 
     1       781258   rs2980314      1       852772  rs28587382            1 
     1       781258   rs2980314      1       858496  rs13303029            1 
     1       791853   rs6684487      1       864755   rs2340589     0.453392 
     1       799463   rs4245756      1       864755   rs2340589     0.252273 
     1       808769  rs12086311      1       852772  rs28587382            1

Thanks

[WouterDeCoster]

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Answer 1

[WouterDeCoster]

LD is always calculated between two SNPs, so you have a SNP-A and a SNP-B, each with their chromosome (CHR) and basepair location (BP). The strength of the LD is calculated as the R^2.