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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