[Bioc-devel] S4 classes extending GRangesList

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

--
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