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

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]]