Hi all, I have several results of a CGH analysis, where a statistic is plotted vs the chromosomes length. Does anybody know if there's a way to plot a graphical representation of each chromosome, with the regions etc etc, so I can overlay it with my plot and directly compare which area of the plot corresponds to which region of the chromosome ? It would be great to have directly a way where i can impute the statistic, the BP and the chr number and to obtain the plot together with the regions of the chromosome. Any suggestion or idea would be appreciated... thanks in advance, Giulio _________________________________________________________________ [[alternative HTML version deleted]]

On Thu, Mar 19, 2009 at 8:09 AM, Giulio Di Giovanni < perimessaggini@hotmail.com> wrote: > > Hi all, > > > > I have several results of a CGH analysis, where a statistic is plotted > vs the chromosomes length. Does anybody know if there's a way to plot a > graphical representation of each chromosome, with the regions etc etc, > so I can overlay it with my plot and directly compare which area of > the plot corresponds to which region of the chromosome ? > I'm not sure what you mean by "regions of the chromosome", but you might want to look at the idiogram, GenomeGraphs, and rtracklayer packages as a start. > > It would be great to have directly a way where i can impute the > statistic, the BP and the chr number and to obtain the plot together > with the regions of the chromosome. > Any suggestion or idea would be appreciated... > > thanks in advance, > > Giulio > > > _________________________________________________________________ > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Hi Giulio, The paintCytobands() function of the quantsmooth package gives nice pictures of chromosomes. Also the idiogram and geneplotter packages help in visualizing genomic information. Jan > > > I have several results of a CGH analysis, where a statistic is plotted > vs the chromosomes length. Does anybody know if there's a way to plot a > graphical representation of each chromosome, with the regions etc etc, > so I can overlay it with my plot and directly compare which area of > the plot corresponds to which region of the chromosome ? > > It would be great to have directly a way where i can impute the > statistic, the BP and the chr number and to obtain the plot together > with the regions of the chromosome. > Any suggestion or idea would be appreciated... > > thanks in advance, > > Giulio > >