[BioC] unexpected result of rep(Rle(), times=<vector or Rle>)

[Patrick Aboyoun]

Chuck,
This was an oversight on my part. I was focused on long Rle vectors and 
didn't fully test when the 'times' argument was an integer vector with 
the same length as 'x'. I just checked in a patch to the IRanges package 
in BioC 2.5 (R 2.10) and BioC 2.6 (R-devel). Given that you are using 
BioC 2.5, you will need IRanges version 1.4.11 or greater. It will be 
available via biocLite in the next 24 hours or so. If you need it 
sooner, you can check it out directly via svn from the Bioconductor 
repository.

 > suppressMessages(library(IRanges))
 > x <- rep(1:4,c(1,2,1,2))
 > Rle(rep(x,x))
'integer' Rle of length 16 with 4 runs
  Lengths: 1 4 3 8
  Values : 1 2 3 4
 > rep(Rle(x), x)
'integer' Rle of length 16 with 4 runs
  Lengths: 1 4 3 8
  Values : 1 2 3 4
 > sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8   
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8  
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] IRanges_1.4.11


Patrick



Charles C. Berry wrote:
>
> Using IRanges_1.4.0 here (checked elsewhere with 1.4.8):
>
> I would expect
>
>     rep( Rle(x), times=Rle(x) ) == Rle( rep(x, x) )
>
> but
>
>> x <- rep(1:4,c(1,2,1,2))
>> Rle(rep(x,x))
> 'integer' Rle of length 16 with 4 runs
>   Lengths:  1 4 3 8
>   Values :  1 2 3 4
>> rep(Rle(x),times=Rle(x))
> 'integer' Rle of length 18 with 4 runs
>   Lengths:  1 5 3 9
>   Values :  1 2 3 4
>> rep(Rle(x),times=x)
> 'integer' Rle of length 18 with 4 runs
>   Lengths:  1 5 3 9
>   Values :  1 2 3 4
>>
>
> Is this the intended behavior?
>
> If so, why?
>
> Chuck
>
>
>
> Charles C. Berry                            (858) 534-2098
>                                             Dept of Family/Preventive 
> Medicine
> E mailto:cberry at tajo.ucsd.edu                UC San Diego
> http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 
> 92093-0901
>
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