Xiaokuan, oligo doesn't offer a copy number tool (yet). However, the results you get from snprma() (summaries for alleles A and B) are the starting point for copy number analysis, which may be of use for you (note that total copy numbers are often estimated from alleleA+alleleB). b On 26 November 2011 20:46, Xiaokuan Wei <weixiaokuan at="" yahoo.com=""> wrote: > Vincent, > > Thank you for your prompt response. > I have checked the "oligo" package before. However, it seems lack of functions to infer total copy number, allelic specific and region specific. (I think dChip has such functions, but I can not find R package for dChip). > Could you let me know if there is any function in "oligo" can carry out such tasks? > Thank you. > > -Xiaokuan > > > ________________________________ > ?From: Vincent Carey <stvjc at="" channing.harvard.edu=""> > > Cc: bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Sent: Saturday, November 26, 2011 8:21 AM > Subject: Re: [BioC] solution for affy human 500k mapping snp array > > > I can't comment on popularity, but the vignetttes listed at > > http://www.bioconductor.org/packages/release/bioc/html/oligo.html > > address processing of these arrays for genotyping. > > > > e: > > Dear list, >> >>I am trying to analyze a set of affy human 500k mapping snp arrays. I try to make copy number calls and relate them to candidate genes. >>I am wondering: what is the most popular package for such a task? >> >> >>Thank you. >> >>Xiaokuan >>? ? ? ?[[alternative HTML version deleted]] >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at 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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >