How to draw LDheapmap using plink.ld result

Question

[mmh7272]

Hi i am beginner Bioinfo

I analysis linkage disequilibrium(ld), from plink

plink.ld result below that

CHR_A         BP_A SNP_A  CHR_B         BP_B SNP_B           R2
     3     30780810    .      3     30780827    .     0.996637
     3     30780810    .      3     30780907    .     0.479487
     3     30780810    .      3     30781157    .     0.715143
     3     30780810    .      3     30781205    .     0.692494
     3     30780827    .      3     30780907    .     0.468367

I wanna try draw LD heatmap using plink.ld result file like haploview plot

Please help me

[mmh7272]

thank you for ur advice!

Answer 1

[Kevin Blighe]

There are quite a few old threads on this topic, but some out of date. I tried to aggregate some of these methods in my recent answer, here: A: Manhattan plots and linkage disequilibrium heatmap

Essentially, you can export your PLINK data to HaploView format, and then easily compute LD and generate a LDheatmap. Given the data that you have, currently, you could probably generate the LDheatmap manually, too.

Please see the related StackOverflow thread, too: https://stackoverflow.com/questions/56118669/manhattan-plot-and-linkage-disequilibrium-heatmap-on-one-plot

Kevin