Aaron,
shift() currently doesn't respect strand because the most common use
case for the function is to change from a 0-based index system to a
1-based index system, which is strand independent. The shift argument to
the shift function, however, does accept an integer vector so you could
use the following code, or something similar, to perform this operation
somewhat efficiently:
amount <- strand(g1)
runValue(amount) <- ifelse(runValue(amount) == "-", -1L, 1L)
shift(g1, as.vector(amount))
Perhaps this can be made simpler in the future if more users what
strand-dependent shifting.
Patrick
On 8/25/10 9:54 PM, Aaron Statham wrote:
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
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