search for: makegenotypes

...vert removed, given that it is an object of type character? Thanks in advance, Neil Background ======== This is a refined example from a larger problem that I'm working on. Given a data frame of pairs of columns containing genotype data I would like to convert them to genotype objects using makeGenotypes. The number of loci (i.e. ncol() / 2) is variable, so I like to be able to determine how many loci there are and then convert all of them. Thus an example data set would be... <-----Start test.dat------> ID,rs1.1,rs1.2,rs2.1,rs2.2,rs3.1,rs3.2,rs4.1,rs4.2,rs5.1,rs5.2,rs6.1,rs6.2 A0001,1,1,1,...

Dear experts, For the makeGenotype function I need a list as in the example. However, since my list needs to be 184 long there must be an easy way to make it. >list(1:2,3:4,5:6,7:8) [[1]] [1] 1 2 [[2]] [1] 3 4 [[3]] [1] 5 6 [[4]] [1] 7 8 I have tried lis<-1:184 dim(lis)=c(92,2,1) as.list(lis) and several other options. Any suggestions? many thanks Marco [[alternative

...;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 M...

I have been merrily using the genetics package and more specifically have been using the makeGenotypes and genotypes function. I check my accomplishments by going > class(g2) [1] "genotype" "factor" and likewise > class(g1) [1] "genotype" "factor" Yet when I execute a command such as allele count I get this > allele.count(g1) D I [1,] 2...