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

[Valerie Obenchain]

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.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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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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