Entering edit mode
Hi,
I just noticed that a piece of logic I was relying on with GRanges
before
does not seem to work anymore. Namely, I expect the behavior of
nearest()
with a single GRanges object as an argument to be the same as that of
IRanges (example below), but it's not anymore. I expect nearest(GR1)
NOT
to behave trivially but to return the closest range OTHER than the
range
itself. I could swear that was the case before, but isn't any longer:
> z=IRanges(start=c(1,5,10), end=c(2,7,12))
> z
IRanges of length 3
start end width
[1] 1 2 2
[2] 5 7 3
[3] 10 12 3
> nearest(z)
[1] 2 1 2
>
> z=GRanges(seqnames=rep('chr1',3),ranges=IRanges(start=c(1,5,10),
end=c(2,7,12)))
> z
GRanges with 3 ranges and 0 elementMetadata cols:
seqnames ranges strand
<rle> <iranges> <rle>
[1] chr1 [ 1, 2] *
[2] chr1 [ 5, 7] *
[3] chr1 [10, 12] *
---
seqlengths:
chr1
NA
> nearest(z)
[1] 1 2 3
>
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] datasets utils grDevices graphics stats methods base
other attached packages:
[1] GenomicRanges_1.8.6 IRanges_1.14.3 BiocGenerics_0.2.0
loaded via a namespace (and not attached):
[1] stats4_2.15.0
>
I want the IRanges behavior and not what seems currently to be the
GRanges
behavior, since I have some code that depends on it. Is there a quick
way
to make nearest() do that for me again?
Thanks!
Oleg.
[[alternative HTML version deleted]]
