[Bioc-devel] isActiveSeq deprecated

[Hervé Pagès]

Note that currently it's kind of inconsistent anyway because it doesn't
look at the seqlevels that are in use. For example:

   library(TxDb.Hsapiens.UCSC.hg19.knownGene)
   txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

Trying to drop chrUn_gl000249 (which I know is not in use):

   > seqlevels(txdb) <- setdiff(seqlevels(txdb), "chrUn_gl000249")
   Error in .seqinfo.TranscriptDbReplace(x, new2old = new2old, force = 
force,  :
     You need to use force=TRUE if you want to drop seqlevels.

'force=TRUE' should only be required when trying to drop seqlevels
that are in use.

So the choice are more between: (a) consistent, (b) convenient,
or (c) leave it as it is (which is neither convenient or consistent).

I vote for (b).

H.


On 09/18/2013 11:31 AM, Marc Carlson wrote:
> I actually considered this, but I opted to do it this way just for the
> sake of being consistent (which was my whole mission for implementing
> seqlevels in here in the 1st place).  Now I could make it more
> convenient here and break consistency with how it is used elsewhere, but
> what do people prefer?
>
> Consistent or convenient?
>
>
>    Marc
>
>
>
> On 09/18/2013 10:40 AM, Hervé Pagès wrote:
>> Hi Marc,
>>
>> Wouldn't it make sense to just ignore the 'force' arg when
>> dropping the seqlevels of a TranscriptDb?
>>
>> The 'force' argument is FALSE by default and this prevents
>> seqlevels<- to shrink GRanges or other vector-like objects
>> when the user tries to drop seqlevels that are in use.
>> Internally seqlevels<- calls seqlevelsInUse() to get the
>> seqlevels currently in use and see if they intersect with
>> the seqlevels to drop.
>>
>> In the TranscriptDb situation, people always have to use
>> 'force=TRUE' to drop seqlevels, regardless of whether the
>> levels to drop are in use or not (the seqlevelsInUse()
>> getter not being defined for TranscriptDb objects, I suspect
>> seqlevels<- doesn't look at this).
>>
>> So maybe 'force' could just be ignored for TranscriptDb objects?
>> That would make seqlevels<- a little bit more user-friendly on
>> those objects.
>>
>> Thanks,
>> H.
>>
>>
>> On 09/13/2013 10:38 AM, Marc Carlson wrote:
>>> Hi Florian,
>>>
>>> Yes we are trying to make things more uniform.  seqlevels() lets you
>>> rename as well as deactivate chromosomes you want to ignore, so it was
>>> really redundant with isActiveSeq().  So we are moving away from
>>> isActiveSeq() just so that users have less to learn about.  The reason
>>> why isActiveSeq was different from seqlevels was just because it was
>>> born for a TranscriptDb (which is based on an annotation database)
>>> instead of being born on a GRanges object.  So seqlevels was the more
>>> general tool.
>>>
>>>     Marc
>>>
>>>
>>>
>>> On 09/13/2013 07:24 AM, Hahne, Florian wrote:
>>>> Hi Marc,
>>>> I saw these warnings in Gviz, but they stem from GenomicFeatures
>>>>
>>>> Warning messages:
>>>> 1: 'isActiveSeq' is deprecated.
>>>> Use 'seqlevels' instead.
>>>> See help("Deprecated") and help("GenomicFeatures-deprecated").
>>>> 2: 'isActiveSeq' is deprecated.
>>>> Use 'seqlevels' instead.
>>>> See help("Deprecated") and help("GenomicFeatures-deprecated").
>>>> 3: 'isActiveSeq<-' is deprecated.
>>>> Use 'seqlevels' instead.
>>>> See help("Deprecated") and help("GenomicFeatures-deprecated").
>>>> 4: 'isActiveSeq<-' is deprecated.
>>>> Use 'seqlevels' instead.
>>>> See help("Deprecated") and help("GenomicFeatures-deprecated").
>>>> 5: 'isActiveSeq' is deprecated.
>>>> Use 'seqlevels' instead.
>>>> See help("Deprecated") and help("GenomicFeatures-deprecated").
>>>> 6: 'isActiveSeq<-' is deprecated.
>>>> Use 'seqlevels' instead.
>>>> See help("Deprecated") and help("GenomicFeatures-deprecated").
>>>>
>>>> So has the whole idea of active chromosomes in the data base been
>>>> dropped? I could not find anything in the change notes. Do I get it
>>>> right that you can now do
>>>> seqlevels(txdb, force=TRUE) <- "chr1"
>>>> if you just want the first chromosome to be active?
>>>>
>>>> Florian
>>>>
>>>
>>>
>>>     [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
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>>>
>>
>

-- 
Hervé Pagès

Program in Computational Biology
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