For GRanges x, my naive expectation is that genome(x) returns a length- one tag identifying the genome to which chromosomal coordinates
correspond. The genome() method seems to have sequence-specific semantics, which makes sense, but when we identify sequence with chromosome, it seems too complicated. Is there a use case for a GRanges with sequences from several different genomes? One reason I am inquiring is that I feel it would be nice to have the GRanges show() method report, prominently, the genome in use (or NA if unspecified). This could be accomplished by reporting unique(genome(x)), and perhaps that would be satisfactory. after example(genome) : > seqinfo(txdb) Seqinfo of length 15 seqnames seqlengths isCircular genome CH2L 23011544 FALSE dm3 CH2R 21146708 FALSE dm3 CH3L 24543557 FALSE dm3 CH3R 27905053 FALSE dm3 CH4 1351857 FALSE dm3 ... ... ... ... CH3LHet 2555491 FALSE dm3 CH3RHet 2517507 FALSE dm3 CHXHet 204112 FALSE dm3 CHYHet 347038 FALSE dm3 CHUextra 29004656 FALSE dm3 > genome(seqinfo(txdb)) CH2L CH2R CH3L CH3R CH4 CHX CHU M "dm3" "dm3" "dm3" "dm3" "dm3" "dm3" "dm3" "dm3" CH2LHet CH2RHet CH3LHet CH3RHet CHXHet CHYHet CHUextra "dm3" "dm3" "dm3" "dm3" "dm3" "dm3" "dm3" [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel