[Bioc-devel] GRanges to VRanges coercion

[Thomas Sandmann]

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.

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 !

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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