[Bioc-devel] the character to collapse the geneNames when using the disjointExons function with aggregateGenes=TRUE
Valerie Obenchain
vobencha at fhcrc.org
Wed Jul 31 19:04:21 CEST 2013
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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