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.cast...@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.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. >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org <mailto:Bioc-devel@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]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
