[Bioc-devel] the character to collapse the geneNames when using the disjointExons function with aggregateGenes=TRUE
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.delhomme at 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
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