Fantastic! 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 --------------------------------------------------------------- On Jul 31, 2013, at 10:41 PM, Alejandro Reyes wrote: > Dear all, > > No problem from my side, I can adapt DEXSeq to those changes. > > Best regards, > Alejandro Reyes > >> Mike, Alejandro, >> >> I also wonder about getting rid of the 'exonID' metadata column. This is >> redundant with 'exonic_part_number'. Do you have a preference for keeping >> one or the other? >> >> Valerie >> >> >> On 07/31/2013 10:04 AM, Valerie Obenchain 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 >> > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
