[BioC] Calculate heterozygosity % using SNP genotype data

[Valerie Obenchain]

Take a look at snpStats, SNPchip and genoset packages. Specifically, see
the snpStats Intro Vignette

    http://bioconductor.org/packages/2.11/bioc/html/snpStats.html

Depending on the origin of your data this thread may also be of interest -

    https://stat.ethz.ch/pipermail/bioconductor/2012-May/045636.html

Valerie

On 06/01/2012 02:50 PM, Yadav Sapkota wrote:
> Hello,
>
> I am trying to validate few LOH regions using SNP genotype data. I am
> assuming that if it is a LOH, it will contain predominantly homozygous
> genotypes. For simplicity, I chose 15 SNPs per ~70 kb LOH region.
>
> Now I need to calculate the heterozygosity for LOHs in each samples using
> genotype data of 15 SNPs.
>
> Does anyone know the way to calculate the heterozygous % per sample using a
> set of SNP genotype data?
>
> Your help will be greatly appreciated.
>
> --Yadav
>
> 	[[alternative HTML version deleted]]
>
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