[BioC] LD plots

Boks, M.P.M. M.P.M.Boks at umcutrecht.nl
Wed Jul 9 17:56:26 CEST 2008

Dear R-friends,

I am stuck making an LD plot of a small genotype set:

An exert of my data (genotypes)

V27/V28 V33/V34 V39/V40 V41/V42
1      B/B     B/B     A/A     B/B
2      B/A     B/B     A/B     B/B
3      B/B     B/B     A/A     B/B
4      B/A     B/A     A/B     B/A
5      B/B     B/B     A/A     B/B

I thought he LDheatmap package would be of use


Gives me the desired LD map of the first two columns only.

How do I make it to take all 4 SNP's/colomns?

Your help is highly appreciated,



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