Bsmooth/bsseq (and QuasR, as well) are great for manipulating and analyzing BSseq data, but there's something in this email that I've never really found a great solution for, and that is so-called "profile" or "metagene" plots (the latter is a confusing bit of terminology, given that it is re-used for linear combinations of gene effects in expression studies).
Suppose you wanted to look at the distribution of H3K4me3 or H3K27me3 ChIP-seq density relative to the start of (or exon/intron junctions within, or enhancers whose activity was linked to, ...) transcribed vs. silent genes across a genome. Suppose you also wanted to look at methylation proportions relative to the same positions (again, the idea here is to take a bunch of landmarks and plot a summary statistic describing the behavior of some measurement relative to those landmarks, across the genome). An example of such a plot is on page 23 of the QuasR user's manual. For clarity, here's a link: https://dl.dropboxusercontent.com/u/12962689/profile.png This seems like something that is so incredibly common it ought to be a generic function within BioC somewhere, but I've never found a really easy way to do it. If I want to plot a density matrix mat[x,y] for alhl x and all y, I can call image(mat) or persp(mat) and that's that. Is there something like this within biocGenerics of which I've remained completely ignorant, or... ? If it isn't a generic somewhere, I think I may have to implement one. On Thu, Sep 12, 2013 at 1:32 AM, Alex Gutteridge <al...@ruggedtextile.com>wrote: > On 12.09.2013 08:25, Gia [guest] wrote: > >> Hi, >> I would like to ask if anyone experienced with creating figures from >> BS-Seq methylation data for end analysis of genes (or any genomic >> features), like what was presented in the following link: >> http://www.nature.com/ng/**journal/v39/n1/fig_tab/ng1929_**F4.html<http://www.nature.com/ng/journal/v39/n1/fig_tab/ng1929_F4.html> >> It would be appreciate if you can show how to create this kind of >> figures using any Bioconductor packages. >> Cheers, >> >> -- output of sessionInfo(): >> >> None >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> ______________________________**_________________ >> Bioconductor mailing list >> bioconduc...@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https://stat.ethz.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> >> > > I've only skimmed through that paper but that figure isn't showing BS-Seq > data as far as I can see - it's showing the results of an array / IP based > approach to methylation quantitation. BSmooth is one of the best packages > I've found for manipulating BS-Seq data. If you get your data in there you > could derive analogous statistics (i.e. methylation levels) pretty easily. > Then any of the base plotting functions will give you similar graphs. > > -- > Alex Gutteridge > > > ______________________________**_________________ > Bioconductor mailing list > bioconduc...@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https://stat.ethz.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> > -- *He that would live in peace and at ease, * *Must not speak all he knows, nor judge all he sees.* * * Benjamin Franklin, Poor Richard's Almanack<http://archive.org/details/poorrichardsalma00franrich> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
