[BioC] Summarization by gene or exon or transcript

Steve Lianoglou lianoglou.steve at gene.com
Thu Oct 31 21:19:30 CET 2013


On Thu, Oct 31, 2013 at 1:04 PM, Reema Singh <reema28sep at gmail.com> wrote:
> Hi Steve,
> Thank you for your reply,
> I just want to known what is the idea feature for summarizing read count
> after alignment?. Gene,transcript,exons features from GFF/GTF files are
> frequently used .

If you are asking what the "ideal" format for storing summarized read
counts is, I would have to say that in "the R world" that would be to
use a SummarizedExperiment (it is a class defined in the GenomicRanges

The rowData() of the SummarizedExperiment would contain the GRanges
(or GRangesList) that define where the counts in each row of your
assay are from, and the columns would tell you the counts for a given

You could store your relevant sample data in `colData`, ie. phenotypic
data for each experiment (column), like cell type, perturbation,
whatever. See ?SummarizedExperiment for more info.

If you were asking something else -- sorry, I'm still not getting what
the question is and perhaps someone else can chime in.


Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology

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