Thanks. Seems to be fixed already in devel.

On Wed, Feb 23, 2011 at 12:15 PM, Janet Young <jayoung@fhcrc.org> wrote:

> Hi again,
>
> I noticed that "reduce" gives an error on RangedData objects if there are
> space names that contain no ranges:
>        Error in endoapply(x[, by], FUN) : 'FUN' did not produce an
> endomorphism
>
> I can work around it, but it'd great not to need to do that.  All the
> details are below.
>
> thanks very much,
>
> Janet
>
> -------------------------------------------------------------------
>
> Dr. Janet Young (Trask lab)
>
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Avenue N., C3-168,
> P.O. Box 19024, Seattle, WA 98109-1024, USA.
>
> tel: (206) 667 1471 fax: (206) 667 6524
> email: jayoung  ...at...  fhcrc.org
>
> http://www.fhcrc.org/labs/trask/
>
> -------------------------------------------------------------------
>
>
>
> > library(IRanges,warn.conflicts=F)
>
> > myregions_RD <-
> RangedData(IRanges(start=c(101L,201L,101L,101L),end=c(250L,300L,220L,501L)),space=c("chr1","chr1","chr1","chr2"),strand=c("+","+","+","+")
>   )
>
> > #### this works
> > reduce(myregions_RD)
> RangedData with 2 rows and 1 value column across 2 spaces
>        space     ranges |      strand
>  <character>  <IRanges> | <character>
> 1        chr1 [101, 300] |           +
> 2        chr2 [101, 501] |           +
>
> > ### drop regions that are bigger than 300bp (now there's nothing left on
> chr2)
> > myregions_RD <- myregions_RD[which(width(myregions_RD)<=300),]
>
> > ### this doesn't work - reduce doesn't like a space without any elements
> > reduce(myregions_RD)
> Error in endoapply(x[, by], FUN) : 'FUN' did not produce an endomorphism
>
> > ### workaround - drop the unused space names
> > myregions_RD <-
> RangedData(IRanges(start=start(myregions_RD),end=end(myregions_RD)),space=as.character(space(myregions_RD)),strand=myregions_RD$strand
>   )
>
> > ### now it works
> > reduce(myregions_RD)
> RangedData with 1 row and 1 value column across 1 space
>        space     ranges |      strand
>  <character>  <IRanges> | <character>
> 1        chr1 [101, 300] |           +
>
> > sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] IRanges_1.8.9
>
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>

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