[BioC] plotting BED intervals to TSS regions

[Seb]

awesome, thanks for the answers.
so far the closest thing i found is seqMINER, but i will definitely
try Tengfei approach too!



On Tue, Feb 12, 2013 at 6:22 AM, Jonathan Cairns
<Jonathan.Cairns at cruk.cam.ac.uk> wrote:
> Hi,
>
> For what it's worth, I would also suggest having a look at the package ChIPpeakAnno, since it is designed to map peaks to genes. (I use its functionality to plot histograms of the positions of 5'/3' ends of peaks, relative to TSSs.) However, as far as I know, ChIPpeakAnno cannot do coverage-style plots so you would still need to use Tengfei's workflow for that.
>
> J
>
> ________________________________________
> From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] on behalf of Tengfei Yin [yintengfei at gmail.com]
> Sent: 11 February 2013 22:41
> To: Seb
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] plotting BED intervals to TSS regions
>
> Hi Seb,
>
> I guess before visualization you need to get the summary statistics ready
> first, I got one idea, maybe you could give a try, and I assume the count
> you want is based on a per base resolution
>
> 1. 'import' function in package rtracklayer to import your BED files and
> TSS files as GRanges object into R, ready for analysis.
>
> 2. ?findOverlaps  in package 'GenomicRanges', there are some utilities to
> summarize the overlapping between your BED and TSS region. Then you can
> easily get an answer to your first question: how many falls within your TSS
> region defined.
>
> 3. compute coverage for your imported BED intervals(GRanges object) , that
> will give you an Rle/RleList.  check 'coverage' function in package
> IRanges/GenomicRanges.
>
> 4. then get views on this coverage data with you tss position object.
> please check 'Views' method in GenomicRanges/IRanges.  This step is
> important, better make sure your TSS have equal length window, for example
> 20kb in your case.
>
> 5. Covert this Views to a matrix by using  as.matrix on previous views
> object. You will get a matrix, whose columns correspond to position around
> tss, from -10kb to 10kb, each row correspond to one tss region. If you want
> to summarize over all tss, just use colSums over this matrix.
>
> 6. After you get this summary data, you can use any graphic package in R to
> visualize this data as lines and relabel the x-axis position from -10k to
> 10k.
>
> As far as I know, there is no direct way in bioc to
> import/aggregate/visualize your BED/TSS file together with one or two
> commands to get what you want yet ...
>
> HTH
>
> Tengfei
>
> On Mon, Feb 11, 2013 at 1:45 PM, Seb <seba.bat at gmail.com> wrote:
>
>> hi gurus
>>
>> i have several BED files containing chromosome #, start and end that
>> correspond to overlapping regions of different ChIP Seq experiments.
>> this part was done with Galaxy.
>>
>> i also have a file containing TSS coordinates +/- 10kb.
>>
>> what i want to do is to create a plot to show how many of my
>> overlapping intervals fall within the TSS regions, and, if they do,
>> have on the X axis the distance to the TSS and on the Y axis the
>> number of regions that overlap that certain part of the TSS
>>
>> ...i am a bit confused about how to do this tho...i looked in galaxy
>> and google but i didn't find a clear answer!
>>
>> thanks
>>
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>
>
>
> --
> Tengfei Yin
> MCDB PhD student
> 1620 Howe Hall, 2274,
> Iowa State University
> Ames, IA,50011-2274
>
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