Hi, is there some existing function which can use the biomart gene band information for creating chromosome plots? I've got amplification and deletion frequencies for certain genes. What I would like to do is 1. get the $band info for a list of genes using biomart 2. make a plot for each chromosome which displays the amplification frequencies of the genes as barplot matched to a nice chromosome picture exhibiting the bands. (basically similar to the following picture http://www.biomedcentral.com/1471-2105/5/13/figure/F5) regards, Benjamin

Provided your data is from human, mouse, or rat the idiogram package may be helpful. -kyle > From: Benjamin Otto <b.otto at="" uke.uni-hamburg.de=""> > Date: Thu, 13 Jul 2006 16:49:33 +0200 > To: 'BioClist' <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] Display Chromosome-bands in a plot > > Hi, > > is there some existing function which can use the biomart gene band > information for creating chromosome plots? I've got amplification and > deletion frequencies for certain genes. What I would like to do is > > 1. get the $band info for a list of genes using biomart > 2. make a plot for each chromosome which displays the amplification > frequencies of the genes as barplot matched to a nice chromosome picture > exhibiting the bands. (basically similar to the following picture > http://www.biomedcentral.com/1471-2105/5/13/figure/F5) > > regards, > > Benjamin > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor This email message, including any attachments, is for the so...{{dropped}}

The lodplot package on CRAN has a function to draw chromosome bands, and the quantsmooth package in the Bioconductor development branch has a version of that plot that I've improved to make it more visually appealing. Jan -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Benjamin Otto Sent: donderdag 13 juli 2006 16:50 To: 'BioClist' Subject: [BioC] Display Chromosome-bands in a plot Hi, is there some existing function which can use the biomart gene band information for creating chromosome plots? I've got amplification and deletion frequencies for certain genes. What I would like to do is 1. get the $band info for a list of genes using biomart 2. make a plot for each chromosome which displays the amplification frequencies of the genes as barplot matched to a nice chromosome picture exhibiting the bands. (basically similar to the following picture http://www.biomedcentral.com/1471-2105/5/13/figure/F5) regards, Benjamin _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor