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.cast...@upf.edu <mailto:robert.cast...@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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