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

[Alejandro Reyes]

Dear all,

No problem from my side, I can adapt DEXSeq to those changes.

Best regards,
Alejandro Reyes

> 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
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
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