[Bioc-devel] GRanges to VRanges coercion

[Michael Lawrence]

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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