[Bioc-devel] isActiveSeq deprecated

[Hervé Pagès]

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
>>
>
>
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-- 
Hervé Pagès

Program in Computational Biology
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