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]]

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