[BioC] Genotype imputation

[Antoni Picornell]

Hi Tim,

Thanks a lot for this suggestion. I'm already parsing my inputs in order to 
try it. 

Regards,
Antoni.

> Hi Antoni,
>
> I've been using the snpMatrix package for imputing SNPs which are not
> present on our platform. There's a convenient package vignette to walk
> you through the procedure. I've not tried imputing missing values, so
> I can't comment on that.
>
> Regards,
>
> Tim Rayner
>
> --
> Bioinformatician
> Smith Lab, CIMR
> University of Cambridge
>
> 2009/11/5 Antoni Picornell <urnenfelder at gmail.com>:
> > 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
> >
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