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
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