[BioC] flip strand information in GappedAlignments or GRangesList Object

[Steve Lianoglou]

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

-- 
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