On Thu, Mar 22, 2012 at 10:39 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> wrote: > On Thu, Mar 22, 2012 at 5:36 PM, Javerjung Sandhu <jsandhu at="" bcgsc.ca=""> wrote: > >> Dear Sir or Madam, >> >> I am interested in using Bioconductor to analyze and compare some data >> I?ve recently acquired and was wondering if you could help direct me to an >> appropriate analysis package. >> >> > I have two sets of data, from two separate groups of AML patients. ?One set >> is of 96 patients, the other set is of 178 patients, and I have sequencing >> data for both groups. ?For a few genes of interest the first group?s >> dataset, it looked like there were a number of SNPs that were found with a >> higher than normal frequency among the 96 patients. What I would like to do >> is find out if the frequency of these SNPs is the same in the dataset of >> 178 patients. ?I just need a way of analyzing the frequency of SNPs in a >> large set of sequences. >> > > This question is not very clear. ?If you have already done SNP calling with > your sequences (using samtools or some other external resource) I suppose > it would be typical to have results in VCF format. ?This can be parsed > using VariantAnnotation package, and you can tabulate variants and do some > kind of categorical analysis to compare populations downstream. Some of the > relevant computations for variant tabulation on the basis of VCF are given > in the cgdv17 experimental data package vignette. ?There are no high level > functions that I know of for doing population comparisons, so you should > involve an experienced statistical geneticist if possible. I will second Vince's comment about involving a statistical geneticist; it is really easy to do these types of analyses incorrectly. As for "how to do it" in R, you could take a look at: http://www.genabel.org/tutorials/ABEL-tutorial Outside R, you might take a look at plink. Samtools also has rudimentary association testing capabilities. Sean > If you have not done SNP calling, and your sequence data are in SAM or BAM > format, you could use the pileup manipulations of Rsamtools to enumerate > and tabulate variants. ?Examples of such manipulations in the domain of > transcript variants can be found in the vignette of the ggtut experimental > data package. > > >> Thanks very much, >> Jung >> >> >> >> ? ? ? ?[[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