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 ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
