[BioC] Genotype imputation

Tim Rayner tfrayner at gmail.com
Thu Nov 5 15:54:48 CET 2009


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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>



More information about the Bioconductor mailing list