[Bioc-devel] show method for CompressedVRangesList-class

[Michael Lawrence]

Why not have the SimpleVRangesList be shown like CompressedVRangesList, for
consistency with GRangesList? In other words, the opposite of what you
propose. A strong argument could also be made that a
SimpleGenomicRangesList should be shown like a GRangesList. Unless there is
some aversion to the more verbose output....

On Tue, Feb 24, 2015 at 2:36 PM, Robert Castelo <robert.castelo at upf.edu>
wrote:

>  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.
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
>

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