[BioC] flip strand information in GappedAlignments or GRangesList Object
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Fri Mar 30 14:37:06 CEST 2012
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 =
Incorrect number of arguments (6), expecting 4 for
sessionInfo() pasted below.
R version 2.15.0 RC (2012-03-24 r58823)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 Rsamtools_1.7.41 Biostrings_2.23.6 GenomicRanges_1.7.40
 IRanges_1.13.34 BiocGenerics_0.1.14
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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