[BioC] Plotting data from a bedGraph file

[Michael Hoffman]

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