[Bioc-sig-seq] generic for strand in genomeIntervals and GenomicRanges
Nicolas Delhomme
delhomme at embl.de
Tue Mar 29 14:57:36 CEST 2011
Thanks Michael!
I did not know about the `magic` :-)
There are 2 reasons I use genomeIntervals in parallel to IRanges and rtracklayer.
First, IMO and experience, the readGff3 function is more robust to incorrectly formatted gff files. In addition accessing the attributes is extremely fast using the parseGffAttributes and getGffAttribute functions.
Second, the genomeIntervals had the interval_complement function implemented from the beginning and this has only recently been addressed in IRanges through the gaps function.
Cheers,
Nico
---------------------------------------------------------------
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 29 Mar 2011, at 14:40, Michael Lawrence wrote:
>
>
> On Tue, Mar 29, 2011 at 3:17 AM, Nicolas Delhomme <delhomme at 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 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
> > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> >
> > Location: M1-B861
> > Telephone: 206 667-2793
> >
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