[BioC] flip strand information in GappedAlignments or GRangesList Object

[Steve Lianoglou]

Hi,

On Fri, Mar 30, 2012 at 8:42 AM, Kathi Zarnack <zarnack at ebi.ac.uk> wrote:
> 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.

It's true that sometimes you get bitten by Rle's popping up where you
didn't expect them when you try and index things and need to do some
as.vector() mojo here and there, but in this case it should actually
work (depending on your version of R/bioc, I guess).

In my case (running R-2.15 RC), the Rle "surprise" doesn't catch you
here, but it's still a good idea to keep in mind.

Thanks for pointing that out!

-steve

> 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
>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact