I have SNP Genotype data and I am looking forward to convert it to matrices of 0,1,2. I found the same question in http://www.biostars.org/post/show/15399/how-to-convert-snp-genotype-data-into-012-matrix/ but I am not able to find the answer as what package/software to use. Can someone provide the link for any such conversion tools?
I am not a bioinformatics person; I am basically a software guy. I would also like to know what are the software packages (more specifically an opensource tool written in java or python) that are good in analyzing Genomic SNP data and has reasonable documentation.
I tried to run the following code. But as per the snpMatrix class (http://svitsrv25.epfl.ch/R-doc/library/snpMatrix/html/snp-class.html) I am supposed to have the matrix as SNP class object. Can some one tell me how to convert the variable "val" into an snp matrix?
In short I want to do the inverse of what has been given as solution in this thread (http://www.biostars.org/post/show/14703/updated-r-package-to-analyse-eqtl-and-tutorials-available-for-the-association-of-genetic-variants-and-gene-expression/).
val<- read.table("C:/Users/vineeth/Desktop/Data.txt") val V1 V2 V3 1 GG AA AG 2 GG AA AA 3 AA AA GG
coerce(from=val, to="numeric",strict=TRUE)  "c(2, 2, 1)" "c(1, 1, 1)" "c(2, 1, 3)"