Dario,
Make sure you provide your sessionInfo() when reporting behavior. The
answer to you second issue dealing with the lapply method is due to
symbol masking. The GenomicRanges package uses the implicit generic for
lapply created by the IRanges package. This implicit generic is not the
one you selected when you ran your lapply command. Next time to be sure
you grab the correct lapply function, you can use IRanges::lapply(grl, ...).
> library("GenomicRanges")
> find("lapply")
[1] "package:IRanges" "package:base"
> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-08-01 r52659)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicRanges_1.1.20 IRanges_1.7.15
The first issue you reported is intended. GRanges objects are only bound
if the seqlengths are non-NAs. For example, to get behavior that you are
expecting, set the seqlengths to positive integer values:
> gr <- GRanges("chr2", IRanges(250, 285), strand="-", seqlengths =
c(chr2=300))
> gr
GRanges with 1 range and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] chr2 [250, 285] - |
seqlengths
chr2
300
> resize(gr, 300)
GRanges with 1 range and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] chr2 [1, 285] - |
seqlengths
chr2
300
Warning message:
In `start<-`(`*tmp*`, value = -14L) : trimmed start values to be positive
I hope this helps.
Cheers,
Patrick
On 8/5/10 6:00 PM, Dario Strbenac wrote:
Hi,
I'd like to point out that resize extends beyond the start of a chromosome, for
reads that are close to the start, and on the negative strand.
gr
GRanges with 1 range and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] chr2 [250, 285] - |
resize(gr, 300)
GRanges with 1 range and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] chr2 [-14, 285] - |
seqlengths
chr2
NA
Would the desirable behaviour be to only extend to base 1 ?
One more question. In the user manual (page 12, bottom), it says lapply can be
used on a GRangesList, but it's not working for me.
grl
GRangesList of length 3
$gr1
GRanges with 1 range and 2 elementMetadata values
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> |<integer> <numeric>
[1] chr2 [3, 6] + | 5 0.45
$gr2
GRanges with 2 ranges and 2 elementMetadata values
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> |<integer> <numeric>
[1] chr1 [ 7, 9] + | 3 0.3
[2] chr1 [13, 15] - | 4 0.5
$gr3
GRanges with 2 ranges and 2 elementMetadata values
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> |<integer> <numeric>
[1] chr1 [1, 3] - | 6 0.4
[2] chr2 [4, 9] - | 2 0.1
seqlengths
chr2 chr1
NA NA
lapply(grl, cat, "Hello")
Error in as.list.default(X) :
no method for coercing this S4 class to a vector
--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
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