[BioC] Where to get BAM files for easyRNASeq human use case ALSO ANNOTATION
mtmorgan at fhcrc.org
Fri Aug 17 14:16:14 CEST 2012
On 08/17/2012 04:36 AM, Steve Lianoglou wrote:
> On Friday, August 17, 2012, Wolfgang Huber wrote:
>> On 8/17/12 9:48 AM, Nicolas Delhomme wrote:
> We'd be happy to add methods or converters from SummarizedExperiment to
>> DESeq's CountDataSet and DEXSeq's ExonCountSet classes, presumably into
>> these packages.
>> The problem is the reverse direction: SummarizedExperiment insists on
>> having (non-NA) ranges information (start, end, width), while this is not a
>> restriction that would make sense to impose on count tables for DESeq or
I recently implemented support for no coordinates,
> m = matrix(0, 10, 5, dimnames=list(LETTERS[1:10], letters[1:5]))
> sx = SummarizedExperiment(m) ## etc;
the rowData is a GRangesList of length nrow(m), and with all ranges with
> I'm trying to think of why this restriction doesn't make sense for DESeq
> and co's count tables but I'm drawing a blank.
> The counts in each row of the count table are surely coming from some
> genomic locus, no?
> Are you thinking about thing like gene fusion events or something?
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