Hi Chandu, Alternatively, you can use a combination of readGAlignmentsFromBam/sequenceLayer/consensusMatrix, to generate one consensus matrix per chromosome. See ?sequenceLayer in the Rsamtools package for an example of how to do this. H. On 08/29/2013 01:10 AM, Maintainer wrote: > > > Hi Chandu, > > The 'applyPileups' in the 'Rsamtools' packages will help you here: > > "An array of dimensions nucleotide x file x position. > The ?nucleotide? dimension is length 5, corresponding to ?A?, ?C?, ?G?, > ?T?, and ?N? respectively." (Taken from the 'Rsamtools' manual) > > The coverage you can then get with a function like 'rowSums'. > > Best wishes > Julian > > > On 08/29/2013 09:58 AM, Chandu [guest] wrote: >> >> Hi ALL, >> >> Given BAM file, I like to get output something like below. Any ideas? >> >> >> Chr Position DepthOfCoverage BaseCounts >> chr1 14112 14 A:0 C:0 G:0 T:14 N:0 >> chr1 14113 13 A:0 C:13 G:0 T:0 N:0 >> chr1 14114 11 A:0 C:0 G:0 T:11 N:0 >> chr1 14115 11 A:10 C:0 G:0 T:1 N:0 >> >> Many thanks in advance. >> >> Best Regards >> Chandu >> >> -- output of sessionInfo(): >> >> R version 3.0.0 (2013-04-03) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ at public.gmane.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > ____________________________________________________________________ ____ > devteam-bioc mailing list > To unsubscribe from this mailing list send a blank email to > devteam-bioc-leave at lists.fhcrc.org > You can also unsubscribe or change your personal options at > https://lists.fhcrc.org/mailman/listinfo/devteam-bioc > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319

On 09/03/2013 12:01 PM, Maintainer wrote: > Hi Chandu, > > Alternatively, you can use a combination of > readGAlignmentsFromBam/sequenceLayer/consensusMatrix, > to generate one consensus matrix per chromosome. > See ?sequenceLayer in the Rsamtools package for an example > of how to do this. Forgot to mention that sequenceLayer() is only available in current BioC devel (i.e. BioC 2.13). Cheers, H. > > H. > > > On 08/29/2013 01:10 AM, Maintainer wrote: >> >> >> Hi Chandu, >> >> The 'applyPileups' in the 'Rsamtools' packages will help you here: >> >> "An array of dimensions nucleotide x file x position. >> The ?nucleotide? dimension is length 5, corresponding to ?A?, ?C?, ?G?, >> ?T?, and ?N? respectively." (Taken from the 'Rsamtools' manual) >> >> The coverage you can then get with a function like 'rowSums'. >> >> Best wishes >> Julian >> >> >> On 08/29/2013 09:58 AM, Chandu [guest] wrote: >>> >>> Hi ALL, >>> >>> Given BAM file, I like to get output something like below. Any ideas? >>> >>> >>> Chr Position DepthOfCoverage BaseCounts >>> chr1 14112 14 A:0 C:0 G:0 T:14 N:0 >>> chr1 14113 13 A:0 C:13 G:0 T:0 N:0 >>> chr1 14114 11 A:0 C:0 G:0 T:11 N:0 >>> chr1 14115 11 A:10 C:0 G:0 T:1 N:0 >>> >>> Many thanks in advance. >>> >>> Best Regards >>> Chandu >>> >>> -- output of sessionInfo(): >>> >>> R version 3.0.0 (2013-04-03) >>> Platform: x86_64-apple-darwin10.8.0 (64-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ at public.gmane.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> >> ___________________________________________________________________ _____ >> devteam-bioc mailing list >> To unsubscribe from this mailing list send a blank email to >> devteam-bioc-leave at lists.fhcrc.org >> You can also unsubscribe or change your personal options at >> https://lists.fhcrc.org/mailman/listinfo/devteam-bioc >> > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319