[BioC] rtracklayer and UCSC

[Kasper Daniel Hansen]

As far as I know USCS uses zero-based indexing of their genomes, R  
uses 1-based. What kind of conversion is being used by rtracklayer - I  
suspect none at all? It might be worthwhile to add a discussion about  
this somewhere in the vignette?

More specifically, I have downloaded a couple of tables from UCSC  
using rtracklayer and I wanted to know if I need to add 1 to the  
column named exonStart (after a suitable splitting - it is a comma  
separated character list).

Kasper