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

[Mike Love]

Fine by me. 

I am currently rewriting parathyroidSE to benefit from this and the summarizeOverlaps changes. The workflow is greatly simplified.

Mike

On Jul 31, 2013, at 7:04 PM, Valerie Obenchain <vobencha at fhcrc.org> 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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>