[BioC] Where to get BAM files for easyRNASeq human use case ALSO ANNOTATION

[Martin Morgan]

On 08/17/2012 04:36 AM, Steve Lianoglou wrote:
> Hi,
>
> On Friday, August 17, 2012, Wolfgang Huber wrote:
>
>>
>>
>> On 8/17/12 9:48 AM, Nicolas Delhomme wrote:
>
>
> [snip]
>
> 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
>> DEXSeq.

I recently implemented support for no coordinates,

 > m = matrix(0, 10, 5, dimnames=list(LETTERS[1:10], letters[1:5]))
 > sx = SummarizedExperiment(m) ## etc;
 > class(rowData(sx))
[1] "GRangesList"
attr(,"package")
[1] "GenomicRanges"

the rowData is a GRangesList of length nrow(m), and with all ranges with 
length 0.

Martin

>
>
> Interesting.
>
> 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?
>
> Thanks,
> -steve
>
>
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793