Hi Aditya, It feels that a coercion method from BSgenome to GRanges should rather be defined in the BSgenome package itself. Patch/PR welcome on GitHub. More generally speaking, coercion methods should be defined in a place that is "as close as possible" to the "from" or "to" classes rather than in a package that doesn't own any of the 2 classes involved.
Is this what you have in mind for this coercion? > as(seqinfo(BSgenome.Celegans.UCSC.ce10), "GRanges") GRanges object with 7 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> chrI chrI 1-15072423 * chrII chrII 1-15279345 * chrIII chrIII 1-13783700 * chrIV chrIV 1-17493793 * chrV chrV 1-20924149 * chrX chrX 1-17718866 * chrM chrM 1-13794 * ------- seqinfo: 7 sequences (1 circular) from ce10 genome Thanks, H. On 9/6/19 03:39, Bhagwat, Aditya wrote: > Dear Bioc devel, > > Is it possible to import the BSgenome class without attaching BiocGenerics > (to keep a clean namespace during the development of > multicrispr<https://urldefense.proofpoint.com/v2/url?u=https-3A__gitlab.gwdg.de_loosolab_software_multicrispr&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cXJaaEvfNbOioopXgFWQms1qny1xehFQyb3V3xDy55M&s=MIR-kUeXy9oWokdQxItuG82hrvs0uwP1aBIqNdM-Jrs&e= > >). > > BSgenome <- methods::getClassDef('BSgenome', package = 'BSgenome') > > (Posted earlier on BioC > support<https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124442_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cXJaaEvfNbOioopXgFWQms1qny1xehFQyb3V3xDy55M&s=oBSScH5uD5j0vCAaj4dfWepjiNGtHm9q5gA8eaIudZ4&e= > > and redirected here following Martin's suggestion) > > Thankyou :-) > > Aditya > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cXJaaEvfNbOioopXgFWQms1qny1xehFQyb3V3xDy55M&s=cEojiObibdSuzmh21opvy85DZyRrjtfo1vEMopKWmAg&e= > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel