On Fri, Jun 5, 2009 at 3:18 PM, Michael Hoffman <9qobl2n02@sneakemail.com>wrote:

> 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.
>

Maybe the ideogram package would help?


>
> 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
>
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