Hi again,
I've run into a problem accessing elements of a GRangesList using single
brackets, but only if they have been added using double brackets after the
initial GRanges() call.
Happens in both 2.6 and devel branches.
> g1 <- GRanges("chr1", IRanges(5, width=1))
> glist <- GRangesList(g1)
> glist[[2]] <- g1
> glist[1]
GRangesList of length 1
[[1]]
GRanges with 1 range and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] chr1 [5, 5] * |
seqlengths
chr1
NA
> glist[2]
Error in .bracket.Index(start, nrow(x), rownames(x), asRanges = TRUE) :
range index out of bounds
> glist[[2]]
GRanges with 1 range and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] chr1 [5, 5] * |
seqlengths
chr1
NA
> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-07-06 r52460)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicRanges_1.1.20 IRanges_1.7.24
Thanks,
Aaron
--
Aaron Statham
Postgraduate Scholar, Cancer Epigenetics
Garvan Institute of Medical Research Tel: (02) 9295 8393
384 Victoria St Darlinghurst 2010 Fax: (02) 9295 8316
NSW Australia email: [email protected]
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