[Bioc-devel] show method for CompressedVRangesList-class

 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>
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.