Farrel Buchinsky wrote:> 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?
>
gg1char<-nchar(gg)==1
gg[gg1char]<-paste(gg[gg1char],gg[gg1char],sep="")
Jim