Sequenom has an odd format of calling a SNP genotype
gg
[1] "C" "GA" "A" "C" "C" "AG" "C" "C" "T" "G"
homozygous A is called A and heterozygous is called AT
The genetics package cannot handle the fact that some genotypes are declared
with 2 letter while other are declared with only 1. Consequently the
genotype() or makeGenotypes() will not work.
I need to either find a clever way that the genetics package actually does
do this. I think it may reside in the "method" argument but do not know how
to manipulat it. Alternatively I have to come up with some nifty string
manipulation. Any ideas?
--
Farrel Buchinsky
Mobile: (412) 779-1073
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