[Bioc-devel] GRanges to VRanges coercion

On Thu, Feb 19, 2015 at 12:46 PM, Thomas Sandmann <sandmann.thomas at gene.com>
wrote:

Hi Valerie, hi Michael,

I find myself frequently moving back and forth between data.frames,
GRanges and VRanges objects.

The makeGRangesFromDataFrame function from the GenomicRanges makes the
coercion between the former straightforward, but I couldn't find anything
similar for the second step, coercsion from GRanges to VRanges.

There is a coercion method defined in the GenomicRanges package:

getMethod(coerce, c("GRanges", "VRanges"))
Method Definition:

function (from, to = "VRanges", strict = TRUE)
{
     obj <- new("VRanges")
     as(obj, "GRanges") <- from
     obj
}
<environment: namespace:GenomicRanges>

Signatures:
         from      to
target  "GRanges" "VRanges"
defined "GRanges" "VRanges"

but I haven't been able to get it to work (or find where it is
documented). The source code shown above doesn't indicate how the coercion
method would check for the presence of required / optional VRanges columns,
e.g. 'ref', 'alt', 'altDepth', etc.

This is just the default coercion method added by the methods package for a
conversion of a class to its parent class. It obviously will not do the
right thing, in general.

Would it be useful to add an explicit makeVRangesFromGRanges function to
the VariantAnnotation package ( and / or the corresponding coercion method)
?

Then it would be easy to go from a data.frame to a VRanges object, e.g.
as in this pseudocode:

makeVRangesFromGRanges(
    makeGRangesFromDataFrame( data.frame )
)

You can find a first attempt at implementing the makeVRangesFromGRanges function
here <https://gist.github.com/tomsing1/bf917b1b48afb952e1c5>, which you
are welcome to use / modify if you find it useful.

If this functionality should already be available, I'd be happy to learn
about that, too !

Val, do you think you could review and incorporate Thomas's code? It seems
like a good addition to me.

Thanks,
Michael

Thank you,
Thomas


SessionInfo()

R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (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] stats4    parallel  stats     graphics  grDevices utils     datasets
  methods   base

other attached packages:
  [1] VariantAnnotation_1.12.9 Rsamtools_1.18.2         Biostrings_2.34.1
      XVector_0.6.0            GenomicRanges_1.18.4
  [6] GenomeInfoDb_1.2.4       IRanges_2.0.1            S4Vectors_0.4.0
      BiocGenerics_0.12.1      BiocInstaller_1.16.1
[11] roxygen2_4.1.0           devtools_1.7.0

loaded via a namespace (and not attached):
  [1] AnnotationDbi_1.28.1    base64enc_0.1-2         BatchJobs_1.5
   BBmisc_1.9              Biobase_2.26.0
  [6] BiocParallel_1.0.3      biomaRt_2.22.0          bitops_1.0-6
    brew_1.0-6              BSgenome_1.34.1
[11] checkmate_1.5.1         codetools_0.2-10        DBI_0.3.1
   digest_0.6.8            fail_1.2
[16] foreach_1.4.2           GenomicAlignments_1.2.1
GenomicFeatures_1.18.3  iterators_1.0.7         Rcpp_0.11.4
[21] RCurl_1.95-4.5          RSQLite_1.0.0           rtracklayer_1.26.2
    sendmailR_1.2-1         stringr_0.6.2
[26] tools_3.1.2             XML_3.98-1.1            zlibbioc_1.12.0

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