DeepSNV,Granges and BSgenome question
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Asma rabe ▴ 290
@asma-rabe-4697
Last seen 6.4 years ago
Japan
Dear All, I am trying to run Shearwater and deep SNV to analyze exome-seq data. In the deepSNV vignette #========== ## Load data from deepSNV example regions <- GRanges("B.FR.83.HXB2_LAI_IIIB_BRU_K034", IRanges(start = 3120, end = 3140)) files <- c(system.file("extdata", "test.bam", package = "deepSNV"), system.file("extdata", "control.bam", package = "deepSNV")) counts <- loadAllData(files, regions, q = 10) dim(counts) ## [1] 2 21 10 ## Run (bbb) computes the Bayes factor bf <- bbb(counts, model = "OR", rho = 1e-04) #========== I have two questions: 1-How to create GRnages object for human reference genome, I have used BSgenome package as follows library(BSgenome.Hsapiens.UCSC.hg19) but i do not know how to proceed further for obtaining reference genome as Granges object.. 2-I would like to know how can i specify rho value in Bayes factor calculation. Any help is appreciated. [[alternative HTML version deleted]]
deepSNV deepSNV • 1.2k views
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@michael-lawrence-3846
Last seen 2.5 years ago
United States
On Thu, Jul 10, 2014 at 10:29 PM, Asma rabe <asma.rabe@gmail.com> wrote: > Dear All, > > > I am trying to run Shearwater and deep SNV to analyze exome-seq data. > > > In the deepSNV vignette > > #========== > > ## Load data from deepSNV example > > regions <- GRanges("B.FR.83.HXB2_LAI_IIIB_BRU_K034", IRanges(start = 3120, > end > = 3140)) > > files <- c(system.file("extdata", "test.bam", package = "deepSNV"), > system.file("extdata", > > "control.bam", package = "deepSNV")) > > counts <- loadAllData(files, regions, q = 10) > > dim(counts) > > ## [1] 2 21 10 > > > ## Run (bbb) computes the Bayes factor > > bf <- bbb(counts, model = "OR", rho = 1e-04) > > > #========== > > I have two questions: > > > 1-How to create GRnages object for human reference genome, I have used > BSgenome package as follows > > library(BSgenome.Hsapiens.UCSC.hg19) but i do not know how to proceed > further for obtaining reference genome as Granges object.. > > If you mean that you need a GRanges that spans the entire genome, use: as(seqinfo(Hsapiens), "GRanges") > > 2-I would like to know how can i specify rho value in Bayes factor > calculation. > > Any help is appreciated. > > [[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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