snpStats --- MAF in Pedigrees
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@samuel-younkin-5497
Last seen 9.6 years ago
BioC, I have been using snpStats to analyze case-parent sequence data, and I have found that it would be useful to have a method for the class snpMatrix (along with a pedigree object of some sort) that computed the minor allele frequency in the parents only. Does anyone know if that method exists somewhere for snpMatrix objects? Thanks, Sam
snpStats snpStats • 1.2k views
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@vincent-j-carey-jr-4
Last seen 16 days ago
United States
On Thu, Jan 17, 2013 at 8:50 AM, Samuel Younkin <syounkin@jhsph.edu> wrote: > BioC, > > I have been using snpStats to analyze case-parent sequence data, and I > have found that it would be useful to have a method for the class snpMatrix > (along with a pedigree object of some sort) that computed the minor allele > frequency in the parents only. > > Does anyone know if that method exists somewhere for snpMatrix objects? > > (correct spelling is "SnpMatrix", must avoid confusion with legacy terminology.) I don't know of any immediate solution, but SnpMatrix instances obey X[sample,feature] subscripting, so by indexing to the rows of the parents with P, MAF(X[P,]) should do what you want > Thanks, > > Sam > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
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