On Fri, Jul 20, 2012 at 3:36 PM, gowtham <ragowthaman@gmail.com> wrote:

> Oops!. I think,
> summary(snpmat$genotypes) gave the summary information as in vignette. It
> also has a column with summary on heterozygosity. I assume it summarises
> the data over all the samples.  But, if I would like to know the
> heterozygosity for each of the samples, how do i get that?
>
> And how do I print at the data in snpmat? Sorry for asking such a naive
> question.
>
> Thanks,
> Gowthaman
>
> On Fri, Jul 20, 2012 at 12:19 PM, gowtham <ragowthaman@gmail.com> wrote:
>
> > Hi Everyone,
> > I am attempting to do the same from a vcf file that contains 1000s of
> > variant positions across 4 samples (two groups with 2 replicates each).
> > VCFfiles are generated using GATK.
> >
> > I would like to know what is the heterozygosity levels for each samples.
> I
> > readVcf files and created snpmat using MatrixToSnpMatrix.
> >
> >
> > tab <- TabixFile("./Allsamples_gatk.q_50_30.vcf.gz",
> > "Allsamples_gatk.q_50_30.vcf.gz.tbi")
> > vcf_all <- readVcf(tab, "LdoB")
> > snpmat <- MatrixToSnpMatrix( geno(vcf_all)$GT,
> > values(ref(vcf_all))[["REF"]],
> > library(snpStats)
> > library(hexbin)
> > summary(snpmat)
> >
> > But, summary(snpmat) give different output than that of mentioned in
> > snpStats vignette. I am wondering how do I generate hetrozgosity values
> for
> > each sample here.
> >
> > > summary(snpmat)
> >           Length Class     Mode
> > genotypes 294028 SnpMatrix raw
> > map            4 DataFrame S4
> >
> > The snpmat object seems to be SnpMatrix object with 4 rows and 73507
> > columns. Any further advice will be very much appreciated.
> >
> > Thanks,
> > Gowthaman
> >
> >
> > On Fri, Jun 1, 2012 at 2:50 PM, Yadav Sapkota <ysapkota@ualberta.ca
> >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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> >>
> >
> >
> >
> > --
> > Gowthaman
> >
> > Bioinformatics Systems Programmer.
> > SBRI, 307 West lake Ave N Suite 500
> > Seattle, WA. 98109-5219
> > Phone : LAB 206-256-7188 (direct).
> >
>
>
>
> --
> Gowthaman
>
> Bioinformatics Systems Programmer.
> SBRI, 307 West lake Ave N Suite 500
> Seattle, WA. 98109-5219
> Phone : LAB 206-256-7188 (direct).
>
>         [[alternative HTML version deleted]]
>
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>

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