hi Hervé,
i had not imagine this could require so much code refactoring, so thanks
a lot for the quick and extensive fix. i'll have a close look and let
you know if i encounter any problem.
thanks again!!!
robert.
On 07/20/2017 11:23 AM, Hervé Pagès wrote:
Hi Robert,
This should work in GenomicRanges 1.29.10.
Note that working on this revealed some minor shortcomings
of the GPos internal representation so I decided to change it.
The new one relies on IPos, a new class in IRanges 2.11.10.
IPos is analog to GPos but for "integer positions" instead of
"genomic positions". See ?IPos for the details.
The new GPos objects behave exactly like the old ones except
for 2 things:
- the strand() setter now works
- ranges() now returns an IPos instead of an IRanges
object
Update any old GPos object 'x' with
x <- updateObject(x, verbose=TRUE)
Let me know if you run into any issue with this.
Cheers,
H.
On 07/18/2017 03:00 PM, Robert Castelo wrote:
great, thanks Hervé!
robert.
On 18/07/2017 20:57, Hervé Pagès wrote:
Hi Robert,
I'm working on this.
Best,
H.
On 07/14/2017 02:31 AM, Robert Castelo wrote:
hi,
the strand replacement method for 'GPos' objects does not seem to work:
library(GenomicRanges)
example(GPos)
strand(gpos1) <- "-"
Error in methods::slot(object, name) :
no slot of name "call" for this object of class "GPos"
traceback()
10: methods::slot(object, name)
9: getElement(x, "call")
8: getCall.default(object)
7: getCall(object)
6: update.default(x, strand = value, check = FALSE)
5: update(x, strand = value, check = FALSE)
4: update(x, strand = value, check = FALSE)
3: .local(x, ..., value)
2: `strand<-`(`*tmp*`, value = "-")
1: `strand<-`(`*tmp*`, value = "-")
this kind of operation works perfectly on 'GRanges' objects, so i guess
it should also work also with 'GPos' objects:
example(GRanges)
gr1
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr2 [56, 125] *
-------
seqinfo: 1 sequence from an unspecified genome; no seqlength
strand(gr1) <- "-"
gr1
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr2 [56, 125] -
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
below my session info. thanks!
robert.
ps: sessionInfo()
sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /opt/R/R-3.4.0/lib64/R/lib/libRblas.so
LAPACK: /opt/R/R-3.4.0/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8
[5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
[7] LC_PAPER=en_US.UTF8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicRanges_1.28.3 GenomeInfoDb_1.12.2 IRanges_2.10.2
[4] S4Vectors_0.14.3 BiocGenerics_0.22.0 colorout_1.1-2
loaded via a namespace (and not attached):
[1] zlibbioc_1.22.0 compiler_3.4.0 tools_3.4.0
[4] XVector_0.16.0 GenomeInfoDbData_0.99.0 RCurl_1.95-4.8
[7] bitops_1.0-6
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--
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550
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