On Tue, Mar 29, 2011 at 3:17 AM, Nicolas Delhomme <delhomme@embl.de> wrote:

> 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
>
>

genomeIntervals::`strand<-`(j, factor(rep("+", 4), levels=c("+", "-")))

Btw, I'm kind of curious as to why people are using the both packages at the
same time. What are the use-cases for using one vs. another?

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@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@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >
> >
> > --
> > Computational Biology
> > Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> >
> > Location: M1-B861
> > Telephone: 206 667-2793
> >
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>
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