On Tue, Mar 29, 2011 at 5:57 AM, Nicolas Delhomme <[email protected]> wrote:
> 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. > > I see. rtracklayer has recently gained an argument for choosing specific attributes from GFF, which might help. The support would obviously be better if I actually encountered many GFF files in my daily work. Feedback on e.g. broken files would be appreciated. > 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. > > 'gaps' has been in there since before IRanges even existed, as a method on the IRanges data structure in Biostrings. > Cheers, > > Nico > > --------------------------------------------------------------- > Nicolas Delhomme > > High Throughput Functional Genomics Center > > European Molecular Biology Laboratory > > Tel: +49 6221 387 8310 > Email: [email protected] > 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 <[email protected]> > 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: [email protected] > > 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 [email protected] > > >> 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 > > > > > > _______________________________________________ > > > Bioc-sig-sequencing mailing list > > > [email protected] > > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > > _______________________________________________ > > Bioc-sig-sequencing mailing list > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
