Hi Thomas,
This is addressed in IRanges 1.20.4 (release) and 1.21.7 (devel).
Both should become available thru biocLite() in the next 24 hours
or so.
Cheers,
H.
On 10/28/2013 04:01 PM, Hervé Pagès wrote:
On 10/28/2013 11:16 AM, Hervé Pagès wrote:
Hi Thomas,
Thanks for the report. I'm looking at this. Will let you know
when the problem is fixed.
What has changed in BioC 2.13 is that, by default, the RleList()
constructor now returns a CompressedRleList object instead of a
SimpleRleList object:
return_rles <- RleList(Rle(values=TRUE,lengths=151),
Rle(values=TRUE,lengths=151),
Rle(values=TRUE,lengths=151))
Then:
> class(return_rles) # used to be SimpleRleList (in BioC < 2.13)
[1] "CompressedRleList"
attr(,"package")
[1] "IRanges"
and `[<-` doesn't work (and never has) on a CompressedRleList object
when the subscript is a list-like object:
> return_rles[ list(20:108, 41:131, 21:105) ] <- TRUE
Error in callNextMethod() :
in processing 'callNextMethod', found a '...' in the matched call,
but no corresponding '...' argument
So an immeadiate work-around for you is to call RleList() with
'compress=FALSE' to create a SimpleRleList object:
return_rles <- RleList(Rle(values=TRUE,lengths=151),
Rle(values=TRUE,lengths=151),
Rle(values=TRUE,lengths=151),
compress=FALSE)
Then:
> return_rles[ list(20:108, 41:131, 21:105) ] <- TRUE
This also works with an IRangesList subscript:
keep_ranges <- IRangesList(IRanges(start=20, end=108),
IRanges(start=41, end=131),
IRanges(start=21, end=105))
Then:
> return_rles[ keep_ranges ] <- TRUE
2 issues that need to be addressed:
(1) `[<-` should work on a CompressedRleList object when using a
list-like subscript.
(2) The RleList() constructor should warn that its behavior has
changed when called without specifying the 'compress' arg.
A fix is on its way.
H.
H.
On 10/25/2013 11:33 AM, Thomas Sandmann wrote:
Sorry, forgot that attachments don't make it through.
Here's how to generate the example objects and reproduce the error:
library(IRanges)
keep_ranges <- IRangesList( IRanges( start=20, end=108), IRanges(
start=41,
end=131), IRanges( start=21, end=105))
return_rles <- RleList( Rle(values=TRUE,lengths=151),
Rle(values=TRUE,lengths=151), Rle(values=TRUE,lengths=151))
return_rles[ keep_ranges ] <- TRUE
return_rles[ keep_ranges ] ## subsetting works
return_rles[ keep_ranges ] <- TRUE ## assignment doesn't work
Error in callNextMethod() :
in processing 'callNextMethod', found a '...' in the matched call,
but no
corresponding '...' argument
On Fri, Oct 25, 2013 at 11:23 AM, Thomas Sandmann <sandm...@gene.com>
wrote:
Dear BioC developers,
I am trying to subset an RleList with an IRangesList (see attached
rdata
object). Unfortunately, the following line fails with IRanges 1.20.0:
return_rles[keep_ranges] <- TRUE
Error in subsetListByList_replace(x, i, value) :
cannot subscript an unnamed list-like object by a named list-like
object
Unnaming the IRangesList doesn't help, either:
return_rles[unname(keep_ranges)] <- TRUE
Error in callNextMethod() :
in processing 'callNextMethod', found a '...' in the matched call,
but
no corresponding '...' argument
The same operation worked with IRanges 1.18.2 using the (now
deprecated)
seqselect method:
seqselect( return_rles, keep_ranges ) <- TRUE
Any hints ?
Thanks,
Thomas
SessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
base
other attached packages:
[1] BiocInstaller_1.12.0 IRanges_1.20.0 BiocGenerics_0.8.0
devtools_1.3
loaded via a namespace (and not attached):
[1] digest_0.6.3 evaluate_0.5.1 httr_0.2 memoise_0.1
RCurl_1.95-4.1 stats4_3.0.2 stringr_0.6.2
[8] tools_3.0.2 whisker_0.3-2
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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