Fine by me. I am currently rewriting parathyroidSE to benefit from this and the summarizeOverlaps changes. The workflow is greatly simplified.
Mike On Jul 31, 2013, at 7:04 PM, Valerie Obenchain <voben...@fhcrc.org> wrote: > Hi Nico, > > (Adding Mike and Alejandro.) > > Because disjointExons() came from DEXSeq I wanted to preserve the behavior > for backwards compatibility and familiarity to DEXSeq users. There are a > couple of changes I'd like to make so disjointExons() is consistent with the > other extractors in GenomicFeatures. > > (1) Change metadata column names from 'geneNames' and 'transcripts' to > 'gene_id' and tx_name'. > > (2) Instead of '+' or ';' to separate gene id's or transcript names, these > columns would each be a CharacterList. > > If Mike and Alejandro are ok with these I'll go ahead and implement them. > > Valerie > > > > On 07/31/2013 06:29 AM, Nicolas Delhomme wrote: >> Hej Val, I believe that one is for you :-) >> >> When using the aggregateGenes=TRUE parameter of the disjointExons function, >> the gene names are separated by a "+" character. Is there a particular >> reason for that? The reason I'm asking is that in the "transcripts" column >> the transcripts ID are separated by a semi-column and I was wondering if the >> "separator" could not be unified - i.e. using semi-colon for both the >> geneNames and transcripts column. Here a visual example of what I mean: >> >> GRanges with 1 range and 4 metadata columns: >> seqnames ranges strand | >> <Rle> <IRanges> <Rle> | >> [1] Chr03 [4541747, 4541782] - | >> geneNames >> <character> >> [1] Potri.003G035500+Potri.003G035600+Potri.003G035700 >> transcripts >> <character> >> [1] PAC:26999771;PAC:26999331;PAC:26999330;PAC:26999332;PAC:26999333 >> exonic_part_number exonID >> <integer> <character> >> [1] 1 E001 >> --- >> seqlengths: >> Chr01 Chr02 Chr03 ... scaffold_99 scaffold_991 >> NA NA NA ... NA NA >> >> >> What do you say? >> >> Cheers, >> >> Nico >> >> --------------------------------------------------------------- >> Nicolas Delhomme >> >> Genome Biology Computational Support >> >> European Molecular Biology Laboratory >> >> Tel: +49 6221 387 8310 >> Email: nicolas.delho...@embl.de >> Meyerhofstrasse 1 - Postfach 10.2209 >> 69102 Heidelberg, Germany >> --------------------------------------------------------------- >> >> My sessionInfo()R version 3.0.1 (2013-05-16) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] Rsamtools_1.13.26 Biostrings_2.29.14 DEXSeq_1.7.6 >> [4] GenomicFeatures_1.13.21 AnnotationDbi_1.23.18 Biobase_2.21.6 >> [7] GenomicRanges_1.13.35 XVector_0.1.0 IRanges_1.19.19 >> [10] BiocGenerics_0.7.3 BiocInstaller_1.11.4 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.17.2 bitops_1.0-5 BSgenome_1.29.1 DBI_0.2-7 >> [5] hwriter_1.3 RCurl_1.95-4.1 RSQLite_0.11.4 >> rtracklayer_1.21.9 >> [9] statmod_1.4.17 stats4_3.0.1 stringr_0.6.2 tools_3.0.1 >> [13] XML_3.98-1.1 zlibbioc_1.7.0 >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
