Calculate heterozygosity % using SNP genotype data
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gowtham ▴ 210
@gowtham-5301
Last seen 10.2 years ago
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)$GT, values(ref(vcf_all))[["REF"]], library(snpStats) library(hexbin) summary(snpmat) But, summary(snpmat) give different output than that of mentioned in snpStats vignette. I am wondering how do I generate hetrozgosity values for each sample here. > summary(snpmat) Length Class Mode genotypes 294028 SnpMatrix raw map 4 DataFrame S4 The snpmat object seems to be SnpMatrix object with 4 rows and 73507 columns. Any further advice will be very much appreciated. Thanks, Gowthaman On Fri, Jun 1, 2012 at 2:50 PM, Yadav Sapkota <ysapkota@ualberta.ca> wrote: > Hello, > > I am trying to validate few LOH regions using SNP genotype data. I am > assuming that if it is a LOH, it will contain predominantly homozygous > genotypes. For simplicity, I chose 15 SNPs per ~70 kb LOH region. > > Now I need to calculate the heterozygosity for LOHs in each samples using > genotype data of 15 SNPs. > > Does anyone know the way to calculate the heterozygous % per sample using a > set of SNP genotype data? > > Your help will be greatly appreciated. > > --Yadav > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Gowthaman Bioinformatics Systems Programmer. SBRI, 307 West lake Ave N Suite 500 Seattle, WA. 98109-5219 Phone : LAB 206-256-7188 (direct). [[alternative HTML version deleted]]
SNP snpMatrix SNP snpMatrix • 6.2k views
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gowtham ▴ 210
@gowtham-5301
Last seen 10.2 years ago
Oops!. I think, summary(snpmat$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)$GT, > values(ref(vcf_all))[["REF"]], > library(snpStats) > library(hexbin) > summary(snpmat) > > But, summary(snpmat) give different output than that of mentioned in > snpStats vignette. I am wondering how do I generate hetrozgosity values for > each sample here. > > > summary(snpmat) > Length Class Mode > genotypes 294028 SnpMatrix raw > map 4 DataFrame S4 > > The snpmat object seems to be SnpMatrix object with 4 rows and 73507 > columns. Any further advice will be very much appreciated. > > Thanks, > Gowthaman > > > On Fri, Jun 1, 2012 at 2:50 PM, Yadav Sapkota <ysapkota@ualberta.ca>wrote: > >> Hello, >> >> I am trying to validate few LOH regions using SNP genotype data. I am >> assuming that if it is a LOH, it will contain predominantly homozygous >> genotypes. For simplicity, I chose 15 SNPs per ~70 kb LOH region. >> >> Now I need to calculate the heterozygosity for LOHs in each samples using >> genotype data of 15 SNPs. >> >> Does anyone know the way to calculate the heterozygous % per sample using >> a >> set of SNP genotype data? >> >> Your help will be greatly appreciated. >> >> --Yadav >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- > Gowthaman > > Bioinformatics Systems Programmer. > SBRI, 307 West lake Ave N Suite 500 > Seattle, WA. 98109-5219 > Phone : LAB 206-256-7188 (direct). > -- Gowthaman Bioinformatics Systems Programmer. SBRI, 307 West lake Ave N Suite 500 Seattle, WA. 98109-5219 Phone : LAB 206-256-7188 (direct). [[alternative HTML version deleted]]
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On Fri, Jul 20, 2012 at 3:36 PM, gowtham <ragowthaman@gmail.com> wrote: > Oops!. I think, > summary(snpmat$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]] > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > > > > -- > > 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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@vincent-j-carey-jr-4
Last seen 10 weeks ago
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On Fri, Jul 20, 2012 at 3:19 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. > > use col.summary, not summary > > 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]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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> > > use col.summary, not summary > Thanks Vincent. But, i dont seem to have col.summary function available in my installation. Neigher row.summary. Is it part of snpStats or some basic R package? I managed to get following table. Is it okay to calculate % of heterozygosity (A/B) from here? Or does the calculation originally involves more statistical approach? Thanks once again, Gowthaman -- 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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> library(snpStats) Loading required package: survival Loading required package: splines Loading required package: Matrix Loading required package: lattice Attaching package: 'Matrix' The following object(s) are masked from 'package:IRanges': expand > args(col.summary) function (object, rules = NULL, uncertain = TRUE) NULL give sessionInfo() if questions persist. On Fri, Jul 20, 2012 at 5:11 PM, gowtham <ragowthaman@gmail.com> wrote: > >> use col.summary, not summary >> > > Thanks Vincent. But, i dont seem to have col.summary function available in > my installation. Neigher row.summary. Is it part of snpStats or some basic > R package? > > > I managed to get following table. Is it okay to calculate % of > heterozygosity (A/B) from here? Or does the calculation originally involves > more statistical approach? > > Thanks once again, > Gowthaman > > -- > 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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Too bad on my part Vincent. I have installed the snpStats in the current session but, forgot to load it. I could not believe, i was bothering everyone with having bothered to check this up. Thanks so much for the help, Gowthaman On Fri, Jul 20, 2012 at 3:05 PM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > > library(snpStats) > Loading required package: survival > Loading required package: splines > Loading required package: Matrix > Loading required package: lattice > > Attaching package: 'Matrix' > > The following object(s) are masked from 'package:IRanges': > > expand > > > args(col.summary) > function (object, rules = NULL, uncertain = TRUE) > NULL > > give sessionInfo() if questions persist. > > On Fri, Jul 20, 2012 at 5:11 PM, gowtham <ragowthaman@gmail.com> wrote: > >> >>> use col.summary, not summary >>> >> >> Thanks Vincent. But, i dont seem to have col.summary function available >> in my installation. Neigher row.summary. Is it part of snpStats or some >> basic R package? >> >> >> I managed to get following table. Is it okay to calculate % of >> heterozygosity (A/B) from here? Or does the calculation originally involves >> more statistical approach? >> >> Thanks once again, >> Gowthaman >> >> -- >> 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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