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