[Bioc-devel] GRanges to VRanges coercion

[Valerie Obenchain]

Hi Thomas, Michael,

makeVRangesFromGRanges has been added to 1.13.34. The 
methods-VRanges-class.R file was already large so I added 
makeVRangesFromGRanges.R.

A few notes:

- '...' was replaced with 'keep.extra.columns'

- row names are propagated automatically so I removed the explicit 
row.names(vr)

- Errors are thrown in 2 cases: when arguments are not a single string 
and if 'ref' can't be found. You may want to consider a warning if one 
of the 'field' args can't be found in the GRanges metadata.

- I have not added unit tests. If you have some I'll put them in.

- The function is documented in VRanges-class.Rd. If you want to make a 
stand alone man page similar to makeGRangesFromDataFrame I'll add that too.

Thanks for the contribution Thomas. Nice addition.

Valerie



On 02/20/2015 04:17 PM, Michael Lawrence wrote:
>
>
> On Thu, Feb 19, 2015 at 12:46 PM, Thomas Sandmann
> <sandmann.thomas at gene.com <mailto: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
>
>