[Bioc-devel] Subsetting an RleList object

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 <sandmat1 at 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