Well, it used to work (I use it all the time for parallelizing and
plotting) but I'm not 100% sure if it was documented.  In any event, thanks
much for the fix!

--t


On Sat, Jan 26, 2013 at 2:29 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 01/25/2013 12:19 PM, Tim Triche, Jr. wrote:
>
>> Also, since I almost immediately realized I should try it,
>>
>> R> split(sortedBloodCells, seqnames(rowData(**sortedBloodCells)))$chr9
>> Error in as.vector(x, mode) : invalid 'mode' argument
>>
>> So... that didn't resolve it.
>>
>> Thanks anyone with insight into this.
>>
>
> Hi Tim -- I can't get a working test case in the release or devel branch,
> so I wonder if this ever worked (it would be useful to know, so as to
> understand what changed)? It's now implemented in GenomicRanges 1.11.26
>
>   example("SummarizedExperiment"**)
>
> and then
>
> > split(sset, seqnames(sset))$chr2
> class: SummarizedExperiment
> dim: 150 6
> exptData(0):
> assays(1): counts
> rownames: NULL
> rowData metadata column names(0):
> colnames(6): A B ... E F
> colData names(1): Treatment
>
> Martin
>
>
>
>> --t
>>
>>
>>
>>
>> On Fri, Jan 25, 2013 at 12:18 PM, Tim Triche, Jr. <tim.triche@gmail.com
>> >wrote:
>>
>>  Hi all,
>>>
>>> Were there recent changes in GenomicRanges that might cause this?
>>>
>>> R> class(sortedBloodCells)
>>> [1] "SummarizedExperiment"
>>> attr(,"package")
>>> [1] "GenomicRanges"
>>>
>>> R> showMethods("split")
>>> Function: split (package base)
>>> x="ANY"
>>> x="GRanges"
>>>      (inherited from: x="Vector")
>>> x="RangedData"
>>> x="SummarizedExperiment"
>>>      (inherited from: x="ANY")
>>> x="Vector"
>>>
>>> R> split(rowData(**sortedBloodCells),
>>> seqnames(rowData(**sortedBloodCells)))$chr9
>>> GRanges with 9861 ranges and 0 metadata columns:
>>> ## works fine on the rowData GRanges
>>>
>>> R> split(sortedBloodCells, seqnames(sortedBloodCells))$**chr9
>>> Error in as.vector(x, mode) : invalid 'mode' argument
>>> ## used to be delegated via MM's seqinfo fixes, but now... ?
>>>
>>> R> packageVersion('GenomicRanges'**)
>>> [1] '1.11.24'
>>>
>>>
>>> Thanks,
>>>
>>> --t
>>>
>>>
>>
>>
>>
>
> --
> 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
>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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