[Bioc-devel] show method for CompressedVRangesList-class

[Robert Castelo]

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