[Bioc-devel] Problems with converting GPos to GRanges.
ch@r|e@@p|e@@y @end|ng |rom o|@t@jp
Fri Sep 13 06:29:58 CEST 2019
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:
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
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
Have a nice day,
Charles Plessy - - ~ ~ ~ ~ ~ ~~~~ ~ ~ ~ ~ ~ - - charles.plessy using 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
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