determining linkage between two genomic coordinates
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rna seq ▴ 90
@rna-seq-4145
Last seen 7.6 years ago
Hello, I am trying to determine the linkage association between a set of ~200 coordinates all within about 1Mb of eachother. I would like to create a function that I can enter two locations and have the R^2 value of the linkage association between these two locations returned. I am wondering if anyone can suggest an efficient scheme to accomplish this. TIA [[alternative HTML version deleted]]
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shirley zhang ★ 1.0k
@shirley-zhang-2038
Last seen 9.6 years ago
Dear TIA, SNAP web server might serve your purpose. SNAP allows either SNPid or Genomic Locus as inputs. http://www.broadinstitute.org/mpg/snap/ldsearchpw.php Best, Shirley On Fri, Jul 8, 2011 at 9:23 AM, rna seq <rna.seeker@gmail.com> wrote: > Hello, > > I am trying to determine the linkage association between a set of ~200 > coordinates all within about 1Mb of eachother. I would like to create a > function that I can enter two locations and have the R^2 value of the > linkage association between these two locations returned. I am wondering if > anyone can suggest an efficient scheme to accomplish this. > > TIA > > [[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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Thanks for the link Shirley this is exactly what I am looking for. However, I need something that I can download to my local CPU. On Fri, Jul 8, 2011 at 7:10 AM, shirley zhang <shirley0818@gmail.com> wrote: > Dear TIA, > > SNAP web server might serve your purpose. SNAP allows either SNPid or > Genomic Locus as inputs. > http://www.broadinstitute.org/mpg/snap/ldsearchpw.php > > Best, > Shirley > > On Fri, Jul 8, 2011 at 9:23 AM, rna seq <rna.seeker@gmail.com> wrote: > >> Hello, >> >> I am trying to determine the linkage association between a set of ~200 >> coordinates all within about 1Mb of eachother. I would like to create a >> function that I can enter two locations and have the R^2 value of the >> linkage association between these two locations returned. I am wondering >> if >> anyone can suggest an efficient scheme to accomplish this. >> >> TIA >> >> [[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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