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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