[BioC] flip strand information in GappedAlignments or GRangesList Object

[Kathi Zarnack]

Hi,
I think you have to add vector() to strand(ga), since the strand 
information comes as Rle which does not work in the ifelse() test 
directly. At least this is my experience with GRanges objects.
Best regards,
Kathi

On 30/03/12 13:37, Steve Lianoglou wrote:
> Hi,
>
> On Fri, Mar 30, 2012 at 6:04 AM, Stefanie<stefanie.tauber at univie.ac.at>  wrote:
>> Dear list,
>>
>> having a GappedAlignments or GRangesList object at hand,
>> what is the quickest way to flip strand signs?
>>
>> So for each entry, I want to flip "-" to "+" and vice versa.
> Let's assume that your GappedAlignments object is called `ga`, I think
> this should work, no?
>
> R>  strand(ga)<- ifelse(strand(ga) == '+', '-', '+')
>
> To the devs:
>
> For some reason, `example(GappedAlignments)` is throwing the following
> error on me, so I can't actually test at the moment:
>
> Error in elementLengths(rglist(x)) :
>    error in evaluating the argument 'x' in selecting a method for
> function 'elementLengths': Error in .Call(.NAME, ..., PACKAGE =
> PACKAGE) :
>    Incorrect number of arguments (6), expecting 4 for
> 'cigar_to_list_of_IRanges_by_alignment'
>
> sessionInfo() pasted below.
>
> HTH,
>
> -steve
>
> R version 2.15.0 RC (2012-03-24 r58823)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (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] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] Rsamtools_1.7.41     Biostrings_2.23.6    GenomicRanges_1.7.40
> [4] IRanges_1.13.34      BiocGenerics_0.1.14
>

-- 
Dr. Kathi Zarnack
Luscombe Group
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD, UK
tel +44 1223 494 526