[BioC] Genotype imputation

[Antoni Picornell]

Hello,

I am trying to impute genomic data in one case-control study with 2000 
patients (1000+1000) and Illumina 1M.

I need to perform 2 tasks:
1. Impute missing values in this 1Mx2000 matrix
2. Impute complete genotypes for a list of SNPs that are not in our platform.

As far as I know, this can be done with non-R programs such as impute, mach, 
beagle or even plink (with poor results in this last case). In R we have the 
package GeneABEL, which could be useful in order to obtain the mach input from 
illumina data.

Does anybody knows if there is some package in R that performs these kinds of 
tasks? How do you deal with this issue (even using non-R programs)?

Thanks,
Antoni Picornell