Hi Herv?, 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 <goldstel at gene.com> wrote:
Thanks Herv?. Best wishes, Leonard On Thu, Jun 11, 2015 at 10:58 AM, Herv? Pag?s <hpages at 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
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-- Herv? Pag?s 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: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319