[BioC] Plotting data from a bedGraph file

[Wolfgang Huber]

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
> 
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