Message-ID: <45975E53.8030401@bitwrit.com.au>
Date: 2006-12-31T06:53:07Z
From: Jim Lemon
Subject: Genotype importing from Sequenom
In-Reply-To: <bd93cdad0612302219m5aeeed0fw4cb6bee7621b0244@mail.gmail.com>
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