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.

--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
>



-- 
*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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