[Bioc-devel] isActiveSeq deprecated

[Marc Carlson]

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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