[Bioc-devel] the character to collapse the geneNames when using the disjointExons function with aggregateGenes=TRUE
Nicolas Delhomme
delhomme at embl.de
Fri Aug 2 12:47:34 CEST 2013
Thanks Val!
I've been playing some more with that function and I was wondering if it would make sense to introduce an arguments to filter out synthetic exons if they are smaller than a given size. I.e. In my data I often get 1bp exons, which are obviously of no interest in the downstream analysis. I'm currently doing a post-filtering, but as that could benefit others it may be better if it's directly a function argument. The only issue is that I can't think of a decent default value; i.e. it depends much on the aligner used and on the kind of sequencing data, so it might have to be set to "NULL" by default.
Alejandro - I've seen that in DEXSeq you conserve only these exons you can test - what you call testable exons - does that include a size filter?
What's your take?
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 Aug 2, 2013, at 7:29 AM, Valerie Obenchain wrote:
> These changes are implemented in GenomicFeatures 1.13.26.
>
> Valerie
>
>
> On 08/01/2013 08:45 AM, Nicolas Delhomme wrote:
>> 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
>>>>
>>>
>>
>
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