[BioC] IRanges RangedData - possible bug?

[Patrick Aboyoun]

Janet,
Thanks for reporting this bug. The issue was with the RangedData 
constructor when there was more than one space but less than two spaces 
had information associated with it. I just checked in a fix to the BioC 
2.5 (R 2.10) and BioC 2.6 (R-devel) code lines to address this issue. 
The fixed package version number for BioC 2.5 is 1.4.12 and for BioC 2.6 
is 1.5.55. These packages will become available (and accessible via 
biocLite) at bioconductor.org with the next 48 hours.

Cheers,
Patrick


On 3/5/10 12:24 PM, Janet Young wrote:
> Hi,
>
> I think I've found a bug in the RangedData function, although as 
> always it's
> possible I've misunderstood how the function is supposed to work. 
> There's a
> pretty simple workaround for this issue, but wanted to tell you in 
> case it's
> actually a bug.
>
> The example below explains it pretty succintly, I think, and 
> sessionInfo output
> is at the bottom (on a mac, but I also have the same issue running it 
> on linux
> (with same version of IRanges).
>
> thanks,
>
> Janet Young
>
>
> ##### create simple RangedData object with a score for each object
>
> > rd1 <-
> RangedData(IRanges(start=c(11,31,51),end=c(20,40,60)),
>            space=c("chrA","chrB","chrB"),score=c(5,10,15))
> > rd1
> RangedData with 3 rows and 1 value column across 2 spaces
>         space    ranges |     score
> <character> <IRanges> | <numeric>
> 1        chrA  [11, 20] |         5
> 2        chrB  [31, 40] |        10
> 3        chrB  [51, 60] |        15
>
> ###### filter based on score
>
> > rd1filt <- rd1[rd1[["score"]]>= 10,]
> > rd1filt
> RangedData with 2 rows and 1 value column across 2 spaces
>         space    ranges |     score
> <character> <IRanges> | <numeric>
> 1        chrB  [31, 40] |        10
> 2        chrB  [51, 60] |        15
>
> #### drop the score column - this works fine when more than one object 
> passes
> #### the filter
> #### (I want to drop score column so I can use "reduce" without 
> requiring things
> #### to have matched scores)
>
> > rd1filt_simple <- RangedData(ranges(rd1filt))
> RangedData with 2 rows and 0 value columns across 2 spaces
>         space    ranges |
> <character> <IRanges> |
> 1        chrB  [31, 40] |
> 2        chrB  [51, 60] |
>
> ##### filter more stringently - now I only have one item left
>
> > rd1filt2 <- rd1[rd1[["score"]]>= 15,]
> > rd1filt2
> RangedData with 1 row and 1 value column across 2 spaces
>         space    ranges |     score
> <character> <IRanges> | <numeric>
> 1        chrB  [51, 60] |        15
>
> #### now there's only one range left, the code I was using to drop the 
> score
> #### fails
>
> > RangedData(ranges(rd1filt2))
> RangedData with 1 row and 0 value columns across 2 spaces
> Error in seqselect(values, isplit) :
>   'length(start)' must equal 'length(x)' when 'end' and 'width' are NULL
> Error in args(sessionIno) :
>   no function to return from, jumping to top level
>
> #### the workaround
>
> > rd1filt2_simple <-
> RangedData(IRanges(start=start(rd1filt2),end=end(rd1filt2)),
>                    space=space(rd1filt2))
> > rd1filt2_simple
> RangedData with 1 row and 0 value columns across 1 space
>         space    ranges |
> <character> <IRanges> |
> 1        chrB  [51, 60] |
>
>
> ####### versions:
>
> > sessionInfo()
> R version 2.10.1 (2009-12-14)
> i386-apple-darwin8.11.1
>
> 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_1.4.11
>
> loaded via a namespace (and not attached):
> [1] tools_2.10.1
>
> ##################################
>
>
>
>
> -------------------------------------------------------------------
>
> 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/
>
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