Hello, I am trying to make the CAGEr package (1.27.2) pass its regression tests, and I am still struggling with the refactoring of GPos to UnstitchedGPos and StitchedGPos in the devel branch of Bioconductor...
Currently, my problem is with the following command: promoters(GRanges(CTSScoordinatesGR(exampleCAGEexp))) CTSScoordinatesGR(exampleCAGEexp) returns a GPos object of transcription start sites, that I want to transform in promoter ranges. While it worked in the past, I now have the following error: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘update_ranges’ for signature ‘"UnstitchedIPos"’ I tried the same command with the gpos1a and gpos1b example objects from the GPos manual page, and they do not trigger the error. Further inspection showed me that GRanges(CTSScoordinatesGR(exampleCAGEexp)) returns a GRanges object where the ranges are still in UnstitchedIPos class, while in the case of gpos1a and gpos1b they has been converted. I do not know how to deal with that problem and I would appreciate some help. Have a nice day, Charles -- Charles Plessy - - ~ ~ ~ ~ ~ ~~~~ ~ ~ ~ ~ ~ - - charles.ple...@oist.jp Okinawa Institute of Science and Technology Graduate University Staff scientist in the Luscombe Unit - ~ - https://groups.oist.jp/grsu Toots from work - ~ ~~ ~ - https://mastodon.technology/@charles_plessy _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
