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

[Valerie Obenchain]

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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