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

[Nicolas Delhomme]

Fantastic!

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
---------------------------------------------------------------





On Jul 31, 2013, at 10:41 PM, Alejandro Reyes wrote:

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