[BioC] How to plot NGS data?

[Hahne, Florian]

Just to chime in here:
High up on my list of future developments is some sort of file-based track
class, where all the genomic regions reside on disc in an indexed file,
like BAM, bigWig or tabix. The actual ranges are only realized within R in
the plotting method, so no need to fill the memory with unnecessary
clatter. With the available infrastructure in Rsamtools this should be an
easy extension, I just need to find some time to hack in the code. I guess
some sort of NGS-specific visualization would be the next thing on the
list. There is an experimental AlignedReadsTrack class, but right now
that's really just a huge collection of bugs :-(
Cheers,
Florian


Florian Hahne
Novartis Institute For Biomedical Research
Translational Sciences / Preclinical Safety / PCS Informatics
Expert Data Integration and Modeling Bioinformatics
CHBS, WKL-135.2.26
Novartis Institute For Biomedical Research, Werk Klybeck
Klybeckstrasse 141
CH-4057 Basel
Switzerland
Phone: +41 61 6967127
Email : florian.hahne at novartis.com







On 2/16/12 7:11 AM, "Martin Morgan" <mtmorgan at fhcrc.org> wrote:

>On 02/15/2012 06:14 AM, Bernd Jagla wrote:
>>
>> Hi,
>>
>> I have "a few" reference genomes from NGS resequencing experiments and
>> annotation in GFF format that I would like to use in some of the
>> plotting functions that are available (i.e. geneplotter, ChromHeatMap).
>> Actually, I would to integrate these with expression results from
>> correlated NGS RNA-seq experiments.
>
>Hi Bernd -- maybe good places to start are the ggbio vignette, available
>as a PDF on the page at
>
>http://bioconductor.org/packages/release/bioc/html/ggbio.html
>
>and the Gvis vignette (if you're willing to use the 'devel' version of R
>and Bioconductor)
>
>   http://bioconductor.org/packages/2.10/bioc/html/Gviz.html
>
>Both might give you an idea of the possibilities. library(ShortRead);
>example(Snapshot) might also be a lighter-weight starting point.
>
>If you're able to say more precisely what you'd like, and where you're
>starting from (presumably BAM files, but maybe hints about organism,
>purpose of experiment, what you're hoping to get out of the
>visualization...), perhaps someone on the list will be able to provide
>some more explicit suggestions.
>
>Hope that provides some help. Martin
>
>>
>> My overall approach currently includes using BSGenome,
>> GenenicFeature/FeatureDb, expressionSet and geneplotter/ChromHeatMap.
>>
>> I haven't figured out how to fill an expressionSet class with my counts
>> and how to define regions / genes. Also, is this the class to use? There
>> seem to be too many possible routes to go and I am feeling quite lost...
>>
>> I am now in the process of creating a BSGenome object using
>> BSGenomeForge, which seems to be working.
>>
>> As all this seems to be quite complicated and I haven't found a complete
>> guide on how to visualize NGS results I would like to verify this
>> approach by someone and maybe get some pointers to help me on how to do
>> visualization with RNA-seq experiments...
>>
>> Thanks a lot for your kind help and consideration.
>>
>> Bernd,
>>
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>
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