Hi Malcolm,
The requirement that names of a GRangesList must be unique has actually
been dropped in BioC 2.9 (current devel):
> library(GenomicRanges)
> grl <- GRangesList(a=GRanges(), a=GRanges())
> validObject(grl)
[1] TRUE
Note that before BioC 2.9 this requirement was not only for GRangesList
but also for GRanges objects. In BioC 2.9, this requirement has been
dropped for both containers:
> gr <- GRanges(c("chr1", "chr1"), IRanges(1:2, 4:5, names=c("a", "a")))
> validObject(gr)
[1] TRUE
Cheers,
H.
> sessionInfo()
R Under development (unstable) (2011-07-31 r56578)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicFeatures_1.5.16 GenomicRanges_1.5.21 IRanges_1.11.17
loaded via a namespace (and not attached):
[1] Biobase_2.13.7 biomaRt_2.9.2 Biostrings_2.21.7
[4] BSgenome_1.21.3 DBI_0.2-5 RCurl_1.6-6
[7] RSQLite_0.9-4 rtracklayer_1.13.10 XML_3.4-0
[10] zlibbioc_0.1.7
On 11-08-03 09:23 AM, Cook, Malcolm wrote:
Hi,
re: https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2011-February/001867.html
It appears that the requirement that names of a GRangesList must be unique has
won the day.
I'm not sure I agree with this result, as there are many operations that are
optimized for GRangesList that have use cases that do not depend upon such
uniqueness.
However, I find that such operations can proceed after setting the names to
NULL,, as is demonstrated in the R session following my signature, in which I
am creating a GRanges list with entirely duplicate (unnamed) elements.
I hope this workaround proves useful to others...
Malcolm Cook
Computational Biology - Stowers Institute for Medical Research
Example:
grl=GRangesList(a=GRanges(c(10,20,30),c(15,25,35)),b=GRanges(c(100,200,300),c(150,250,350)))
grl
GRangesList of length 2
$a
GRanges with 3 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] 10 [15, 15] * |
[2] 20 [25, 25] * |
[3] 30 [35, 35] * |
$b
GRanges with 3 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] 100 [150, 150] * |
[2] 200 [250, 250] * |
[3] 300 [350, 350] * |
seqlengths
10 20 30 100 200 300
NA NA NA NA NA NA
grl[rep(1,2)]
Error in `rownames<-`(`*tmp*`, value = c("a", "a")) :
duplicate rownames not allowed
names(grl)=NULL
grl[rep(1,2)]
GRangesList of length 2
[[1]]
GRanges with 3 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] 10 [15, 15] * |
[2] 20 [25, 25] * |
[3] 30 [35, 35] * |
[[2]]
GRanges with 3 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] 10 [15, 15] * |
[2] 20 [25, 25] * |
[3] 30 [35, 35] * |
seqlengths
10 20 30 100 200 300
NA NA NA NA NA NA
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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E-mail: hpa...@fhcrc.org
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