Hi all,
Just ran into this - flank() takes notice of the strand for GRanges objects,
whilst shift() doesn't.
Would it make sense for shift to use the strand in the GRanges method, or is
there a nice alternative? (at the moment I'm doing a shift per strand)
> g1 <- GRanges(rep("chr1", 3), IRanges(rep(5, 3), width=1), c("+","-","*"))
> g1
GRanges with 3 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] chr1 [5, 5] + |
[2] chr1 [5, 5] - |
[3] chr1 [5, 5] * |
seqlengths
chr1
NA
> flank(g1,3)
GRanges with 3 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] chr1 [2, 4] + |
[2] chr1 [6, 8] - |
[3] chr1 [2, 4] * |
seqlengths
chr1
NA
> shift(g1,3)
GRanges with 3 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] chr1 [8, 8] + |
[2] chr1 [8, 8] - |
[3] chr1 [8, 8] * |
seqlengths
chr1
NA
R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu
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_1.0.7 IRanges_1.6.15
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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