Thanks Hervé. Best wishes,
Leonard On Thu, Jun 11, 2015 at 10:58 AM, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi Leonard, > > It's a bug in the "c" method for "CompressedList" object. I'll fix > that. Thanks for the report. > > H. > > > On 06/11/2015 10:48 AM, Leonard Goldstein wrote: >> >> Hi all, >> >> I noticed that when combining instances of a class that inherits from >> GRangesList, the result does not preserve the class (it is returned as >> a GRangesList instead). The class is preserved in other situations >> (e.g. when a class extends GRanges). See below for an example. Is >> there a reason why the class cannot be preserved in the first case? >> Thanks in advance for your help. >> >> Leonard >> >> >>> ## define a new class 'A' inheriting from GRanges >>> setClass(Class = "A", contains = "GRanges") >>> >>> ## combining two instances of class 'A' returns an object of class 'A' >>> gr <- GRanges("1", IRanges(1, 100)) >>> a <- new("A", gr) >>> a >> >> A object with 1 range and 0 metadata columns: >> seqnames ranges strand >> <Rle> <IRanges> <Rle> >> [1] 1 [1, 100] * >> ------- >> seqinfo: 1 sequence from an unspecified genome; no seqlengths >>> >>> c(a, a) >> >> A object with 2 ranges and 0 metadata columns: >> seqnames ranges strand >> <Rle> <IRanges> <Rle> >> [1] 1 [1, 100] * >> [2] 1 [1, 100] * >> ------- >> seqinfo: 1 sequence from an unspecified genome; no seqlengths >>> >>> >>> ## define a new class 'b' inheriting from GRangesList >>> setClass(Class = "B", contains = "GRangesList") >>> >>> ## combining two instances of class 'B' returns a GRangesList >>> grl <- split(gr, 1) >>> b <- new("B", grl) >>> b >> >> B object of length 1: >> $1 >> GRanges object with 1 range and 0 metadata columns: >> seqnames ranges strand >> <Rle> <IRanges> <Rle> >> [1] 1 [1, 100] * >> >> ------- >> seqinfo: 1 sequence from an unspecified genome; no seqlengths >>> >>> c(b, b) >> >> GRangesList object of length 2: >> $1 >> GRanges object with 1 range and 0 metadata columns: >> seqnames ranges strand >> <Rle> <IRanges> <Rle> >> [1] 1 [1, 100] * >> >> $1 >> GRanges object with 1 range and 0 metadata columns: >> seqnames ranges strand >> [1] 1 [1, 100] * >> >> ------- >> seqinfo: 1 sequence from an unspecified genome; no seqlengths >>> >>> >>> sessionInfo() >> >> R Under development (unstable) (2014-11-04 r66932) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats4 parallel stats graphics grDevices utils datasets >> [8] methods base >> >> other attached packages: >> [1] GenomicRanges_1.21.15 GenomeInfoDb_1.5.7 IRanges_2.3.11 >> [4] S4Vectors_0.7.4 BiocGenerics_0.15.2 >> >> loaded via a namespace (and not attached): >> [1] XVector_0.9.1 >>> >>> >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel