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
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--
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
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