[Bioc-devel] isActiveSeq deprecated

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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