On 12/22/2011 05:28 AM, Michael Lawrence wrote: > On Thu, Dec 22, 2011 at 2:46 AM, Jane Merlevede<jane.merlevede@gmail.com>wrote: > >> Thanks for your answer ! >> I'm interesting in using the package that you developed: >> VariantAnnotation. I will try it after installing R.2.14 >> At the beginning of your vignette, you show your data ; there is a column >> "strand". I would like to know if it cares about the strand, because that >> is why I need. I went through your paper and I haven't seen that you >> consider both direct and reverse strand. Does your package handle both >> strands? Or do I need to use the ReverseComplement function first and then >> use your method on only direct strand? >> >> > It uses the strand where sensible, I think. Like in predictCoding(). > Valerie is the ultimate authority; it's really her package. > > Michael Hi Jane, Yes, the methods in VariantAnnotation are strand-aware. They are based on the findOverlaps() function with GRanges or GRangesList objects. By default the 'ignore.strand' argument is FALSE. gr1 <- GRanges("chr1", IRanges(c(5, 10, 20), width=5), strand = c("+", "-", "+")) gr2 <- GRanges("chr1", IRanges(1, 50), strand = "+") findOverlaps(gr1, gr2) findOverlaps(gr1, gr2, ignore.strand = TRUE) Let us know if you have other problems. Valerie > >> Jane Merlevède >> >> >> >> >> 2011/12/20 Michael Lawrence<lawrence.michael@gene.com> >> >>> I think you are looking for the reverseComplement function in Biostrings. >>> Also, the VariantAnnotation package provides much of the functionality of >>> Annovar. >>> >>> Michael >>> >>> On Mon, Dec 19, 2011 at 2:13 AM, Jane Merlevede<jane.merlevede@gmail.com>>>> wrote: >>>> Hello, >>>> >>>> I am looking for "interesting" mutations among a set of mutations. To >>>> reduce the amount of mutations, I am using Annovar. This software takes >>>> as >>>> input a file which contains the following information: chromosome, wild >>>> and >>>> mutated nucleotide(s) and the start and end position of the variant(s). >>>> It seems that this soft use only information from the "direct" sense but >>>> I >>>> have information on reverse strand too. >>>> I wrote a R-script to "reverse" the mutated variants, but I was told that >>>> there is probably a solution to do that in bioconductor. >>>> I haven't found yet, that's why I would like your help to know if it >>>> exists. >>>> >>>> Thanks in advance, >>>> Jane >>>> >>>> [[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]] > > > > _______________________________________________ > 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]]