[Bioc-devel] show method for CompressedVRangesList-class

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
<mailto: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 <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.