On Mon, Jun 7, 2010 at 9:17 AM, pterry@huskers.unl.edu <
pterry@huskers.unl.edu> wrote:

>  Dear bioc-sig-sequencing,
>
> I would like to prepare a display in a browser like that in the 'PeakSeq'
> paper (nat. biotech. 27 66-75 2009, fig 1a, a ChIP-seq signal profile map).
>
> I would like to start by reading into an R session two Eland aligned data
> files to be compared, one the 'treatment', and one the input control
> (chipseq experiment).  For example, for 'trt',
>
> ctcf <- readAligned(cerudataDir, pattern, type="SolexaExport", +
> filter=filt)
>
> Now, how to proceed to my goal in the 1st paragraph?
>
> Perhaps, as in Bioconductor wkshop handout (11/19/09, Seattle), 'A ChIP-Seq
> Data Analysis',
>
> library(BSgenome.Mmusculus.UCSC.mm9)
> mouse.chromlens <- seqlengths(Mmusculus)
> cov.ctcf <- coverage(ctcf, width = mouse.chromlens, extend = 126L)
> yielding a SimpleRleList structure, or
>
> cov.ctcf$chr10
> yielding an Rle structure
>
> Then, perhaps could generate a bed ('bedGraph') (per chromosome) file with
> four columns: chromosome, start, end, and score (here the scores are the
> read depths above each nucleotide).  To save space in the bedGraph file,
> each 'run' of nucleotides from the Rle structure might appear in one record?
>
> Can someone suggest if this is an appropriate approach, and if so, how to
> carry it through to a bed (bedGraph) file?  Or if ill-advised, suggest an
> alternative?
>
>
See the rtracklayer package. If you look through the Bioc course notes,
there are talks on rtracklayer that cover almost exactly this task.

Something like:

session <- browserSession()
session$coverage <- cov.ctcf

Michael


>
> Thanks,
> pterry@huskers.unl.edu
> P. Terry
>
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