The GenomeSearching vignette promises that injecting known SNPs into chromosome sequences is coming soon. I am sorry to be pesky, but may I ask just how soon? I'd love to use this feature now. Best, - Paul

this already exists. see BSgenome::injectSNPs On Sun, Feb 1, 2009 at 2:39 AM, Paul Shannon <pshannon@systemsbiology.org>wrote: > The GenomeSearching vignette promises that injecting known SNPs into > chromosome sequences is coming soon. I am sorry to be pesky, but may I ask > just how soon? I'd love to use this feature now. > > Best, > > - Paul > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Hi Paul, Thanks for the reminder! The feature is already implemented (see ?injectSNPs from the BSgenome software package) and documented, but section "Injecting known SNPs in the chromosome sequences" of the GenomeSearching vignette still needs to be written. I'll complete this vignette before the next BioC release (April). Note that we only provide SNPlocs.Hsapiens.dbSNP.20071016 for now and that it is a little bit outdated but we can add more SNPlocs pkgs if needed (as long as the data are provided by dbSNP). Cheers, H. Paul Shannon wrote: > The GenomeSearching vignette promises that injecting known SNPs into > chromosome sequences is coming soon. I am sorry to be pesky, but may I > ask just how soon? I'd love to use this feature now. > > Best, > > - Paul > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319