[Bioc-sig-seq] generic for strand in genomeIntervals and GenomicRanges

[Nicolas Delhomme]

Hi Martin,

But how would you do for the "replacement" functions, i.e. strand<- ?

The following does not work:

library(genomeIntervals)
j <- new(
               "Genome_intervals_stranded",
               matrix(
                      c(1,2,  
                        3,5,
                        4,6,
                        8,9
                        ),
                      byrow = TRUE,
                      ncol = 2
               ),
               closed = matrix(
                                      c(
                                              FALSE, FALSE,
                                              TRUE, FALSE,
                                              TRUE, TRUE,
                                              TRUE, FALSE
                                       ),
                                      byrow = TRUE,
                              ncol = 2
                              ),
           annotation = data.frame(
                                      seq_name = factor( c("chr01","chr01", "chr02","chr02") ),
                                              strand = factor( c("+", "+", "+", "-") ),
                                              inter_base = c(FALSE,FALSE,FALSE,TRUE)
                                              )
               )

> genomeIntervals::strand(j)<-factor(rep("+",4),levels=c("+","-"))
Error in genomeIntervals::strand(j) <- factor(rep("+", 4), levels = c("+",  : 
  invalid function in complex assignment

Cheers,

Nico


> sessionInfo()
R version 2.12.2 (2011-02-25)
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=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] genomeIntervals_1.6.0 Biobase_2.10.0        intervals_0.13.3     

loaded via a namespace (and not attached):
[1] tools_2.12.2
>

---------------------------------------------------------------
Nicolas Delhomme

High Throughput Functional Genomics Center

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------




On 28 Mar 2011, at 19:42, Martin Morgan wrote:

> On 03/28/2011 05:11 AM, Julien Gagneur wrote:
>> Hi,
>> 
>> both genomeIntervals and the more recent GenomicRanges define a
>> generic method 'strand'. There is the same issue for the method
>> 'reduce' between IRanges and 'Intervals' (which is on CRAN, not on
>> Bioconductor). This leads to conflicts for users that load both
>> packages. Below sample code (the same happens on R 2.13 devel).
>> 
>> How shall we solve that?
> 
> In general, specify the package from which the generic comes from
> 
> GenomicRanges::strand
> genomeIntervals::strand
> 
> It would in general be nice to coordinate generics across packages, but the prospects for that in this particular case are unclear -- genomeIntervals and GenomicRanges have pretty independent and more-or-less mutually exclusive dependencies.
> 
> Martin
> 
>> 
>> Thanks for your advices,
>> 
>> Julien Gagneur
>> 
>> 
>> 
>> 
>>> library(GenomicRanges)
>> Loading required package: IRanges
>> 
>> Attaching package: 'IRanges'
>> 
>> The following object(s) are masked from 'package:base':
>> 
>> Map, cbind, eval, mapply, order, paste, pmax, pmax.int, pmin,
>> pmin.int, rbind, rep.int, table
>> 
>>> library(genomeIntervals)
>> Loading required package: intervals
>> 
>> Attaching package: 'intervals'
>> 
>> The following object(s) are masked from 'package:IRanges':
>> 
>> reduce
>> 
>> 
>> Attaching package: 'genomeIntervals'
>> 
>> The following object(s) are masked from 'package:GenomicRanges':
>> 
>> strand, strand<-
>> 
>>> grngs = GRanges(seqnames=c("chr1", "chr2"),
>>> ranges=IRanges(start=1:2, end=2:3), strand=c("+","-"))
>>> strand(grngs)
>> Error in function (classes, fdef, mtable)  : unable to find an
>> inherited method for function "strand", for signature "GRanges"
>>> reduce(grngs)
>> Error in function (classes, fdef, mtable)  : unable to find an
>> inherited method for function "reduce", for signature "GRanges"
>> 
>>> sessionInfo()
>> R version 2.12.1 (2010-12-16) Platform:
>> x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>> 
>> locale: [1] C
>> 
>> attached base packages: [1] stats     graphics  grDevices utils
>> datasets  methods   base
>> 
>> other attached packages: [1] intervals_0.13.1    GenomicRanges_1.2.3
>> IRanges_1.8.9
>> 
>> loaded via a namespace (and not attached): [1] Biobase_2.10.0
>> genomeIntervals_1.7.4 tools_2.12.1
>> 
>> _______________________________________________ Bioc-sig-sequencing
>> mailing list Bioc-sig-sequencing at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> 
> 
> -- 
> Computational Biology
> Fred Hutchinson Cancer Research Center
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> 
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