[BioC] Plotting data from a bedGraph file

[Michael Hoffman]

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
>>
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