Thanks to Wolfgang and Michael for your helpful replies. GenomeGraphs is a lot closer to what I'm looking for, but I have almost 2 million regions and it seems a bit slow in dealing with large numbers of data rows. I think I will stick with using lattice and xyplot() which is fast enough. This is still useful information for the future though. Thanks. Michael Wolfgang Huber wrote: > Hi Michael > > have you considered the GenomeGraphs (and possibly, rtracklayer) packages? > > Best wishes > Wolfgang > > ------------------------------------------------ > Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber > > > Hoffman ha scritto: >> I have a couple of bedGraph files (similar to wiggle tracks in BED >> style) with scores associated with almost every region of the human >> genome. I have been comparing these with the UCSC genome browser but I >> would prefer to look at all chromosomes simultaneously. >> >> I considered compare them visually with something like cPlot() in >> geneplotter. But at first glance, by reading through some examples >> this appears to be more appropriate for microarray data rather than >> arbitrarily defined genomic regions. Eventually I just read in the >> data like this: >> >> gm12878 <- read.table(gzfile("gm12878.bedGraph.gz"), col.names = >> c("chrom", "chromStart", "chromEnd", "dataValue"), skip=1) >> >> Then I can use xyplot(dataValue ~ chromStart | chrom, gm12878) for a >> crude approximation of what I want. But I was wondering if there was >> something out there a little more polished, whether in Bioconductor (I >> was hoping) or elsewhere. >> >> Thanks! >> >> Michael Hoffman >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 >