[R] Linkage disequilibrium plot

Sabine Siegert sabine.siegert at uni-koeln.de
Thu Sep 11 10:18:16 CEST 2014


I want to generate a LD plot that looks like the triangle in the lower part
of the output of snp.plotter()

As I would not use the values of the original LD measure (instead I use a
more general measure) I have calulated pairwise "correlation" on my own. I
could arrange the results in a data frame like

chr1 pos1 snp1 chr2 pos2 snp2 ld

Is there a way/ function to generate a LD plot without prior calculation of
LD done by R?
Which function can I use based on my own calculations?


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