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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