[Bioc-devel] show method for CompressedVRangesList-class

[Michael Lawrence]

If you're storing data on a relatively small number of individuals (say,
hundreds), you should use SimpleVRangesList, not CompressedVRangesList.

On Wed, Feb 25, 2015 at 7:10 AM, Robert Castelo <robert.castelo at upf.edu>
wrote:

> i see you point, the logic i was thinking about is to use a list of
> VRanges objects to hold separately the variants of multiple individuals,
> with one VRanges object per individual.
>
> if i type the name of such a list object on the R shell, having the
> GRangesList show method, i feel i do not see much information because the
> screen just scrolls up tens or hundreds of lines specifiying variants per
> individual. however, the concise appearance of something like a VRangesList:
>
> > vrl
> VRangesList of length 10
> names(32): S1 S2 S3 S4 ... S7 S8 S9 S10
>
> at least suggests the user that the object holding the variants has
> information for 10 samples and belongs to the class 'VRangesList'.
>
> i thought this made general sense but i'm fine if you feel this
> interpretation does not warrant such a change.
>
> cheers,
>
> robert.
>
> On 02/25/2015 01:25 AM, Michael Lawrence wrote:
>
>> 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.
>>>
>>>         _______________________________________________
>>>         Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>>>         mailing list
>>>         https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>>
>>
>>
> --
> Robert Castelo, PhD
> Associate Professor
> Dept. of Experimental and Health Sciences
> Universitat Pompeu Fabra (UPF)
> Barcelona Biomedical Research Park (PRBB)
> Dr Aiguader 88
> E-08003 Barcelona, Spain
> telf: +34.933.160.514
> fax: +34.933.160.550
>

	[[alternative HTML version deleted]]