[Bioc-devel] show method for CompressedVRangesList-class

[Robert Castelo]

so, yes, but IMO rather than inheriting the show method from a 
GRangesList, i think that the show method for CompressedVRangesList 
objects should be inherited from a VRangesList object. right now this is 
the situation:

library(VariantAnnotation)

example(VRangesList)
vrl
VRangesList of length 2
names(2): sampleA sampleB

cvrl <- new("CompressedVRangesList", split(vr, sampleNames(vr)))
cvrl
CompressedVRangesList object of length 2:
$a
VRanges object with 1 range and 1 metadata column:
       seqnames    ranges strand         ref              alt 
totalDepth       refDepth       altDepth
          <Rle> <IRanges>  <Rle> <character> <characterOrRle> 
<integerOrRle> <integerOrRle> <integerOrRle>
   [1]     chr1    [1, 5]      +           T C             
12              5              7
         sampleNames softFilterMatrix | tumorSpecific
       <factorOrRle>         <matrix> | <logical>
   [1]             a             TRUE |         FALSE

$b
VRanges object with 1 range and 1 metadata column:
       seqnames   ranges strand ref alt totalDepth refDepth altDepth 
sampleNames softFilterMatrix |
   [1]     chr2 [10, 20]      +   A   T         17       10 6           
b            FALSE |
       tumorSpecific
   [1]          TRUE

-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths

would it be possible to have the VRangesList show method for 
CompressedVRangesList objects?

robert.


On 2/24/15 7:24 PM, Michael Lawrence wrote:
> I think you might be missing an import. It should inherit the method 
> for GRangesList.
>
> On Tue, Feb 24, 2015 at 9:53 AM, Robert Castelo 
> <robert.castelo at upf.edu <mailto:robert.castelo at upf.edu>> wrote:
>
>     hi,
>
>     i'm using the CompressedVRangesList class in VariantFiltering to
>     hold variants and their annotations across multiple samples and
>     found that there was no show method for this class (unless i'm
>     missing the right import here) so i made one within
>     VariantFiltering by copying&pasting from other similar classes:
>
>     setMethod("show", signature(object="CompressedVRangesList"),
>               function(object) {
>                 lo <- length(object)
>                 cat(classNameForDisplay(object), " of length ", lo, "\n",
>                     sep = "")
>                 if (!is.null(names(object)))
>                   cat(BiocGenerics:::labeledLine("names", names(object)))
>               })
>
>     i guess, however, that the right home for this would be
>     VariantAnnotation. let me know if you consider adding it there (or
>     somewhere else) and i'll remove it from VariantFiltering.
>
>     thanks,
>
>     robert.
>
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