Great, thank you Hervé. Best wishes,
Leonard On Tue, Sep 29, 2015 at 2:07 PM, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi Leonard, > > Fixed in IRanges 2.3.22 (devel) and 2.2.8 (release). Now the "c" method > for CompressedList objects should always return an object of the same > class as its 1st argument. > > Thanks for your patience and for the reminder. > H. > > > On 09/29/2015 10:35 AM, Leonard Goldstein wrote: >> >> Hi Hervé, >> >> This still looks broken in the current bioc-devel. Just wanted to >> follow up in case it got missed. Thanks again. >> >> Leonard >> >> >> >> On Thu, Jun 11, 2015 at 11:59 AM, Leonard Goldstein <golds...@gene.com> >> wrote: >>> >>> 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 > > > -- > 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