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=""> [[alternative HTML version deleted]]