subject:"\[Bioc\-devel\] IRanges findOverlaps and queryHits"

Re: [Bioc-devel] IRanges findOverlaps and queryHits

2016-12-29 Thread Hervé Pagès

A couple more things about this: The Hits class is defined in the S4Vectors package. The changes to the internals of the class happened in BioC 3.3, almost 1 year ago. The NEWS file in S4Vectors has an entry under "CHANGES IN VERSION 0.10.0" that describes these changes: o Many changes to

Re: [Bioc-devel] IRanges findOverlaps and queryHits

2016-12-20 Thread Michael Lawrence

Hi Nathan, Direct slot access is strongly discouraged, for this very reason. Please stick to using the accessor. And yes, Hits was redefined in terms of a graph model last devel cycle. Michael On Tue, Dec 20, 2016 at 12:16 PM, Nathan Sheffield wrote: > Did the

[Bioc-devel] IRanges findOverlaps and queryHits

2016-12-20 Thread Nathan Sheffield

Did the findOverlaps return object get a @queryHits slot removed recently? I recently got this error running some of my code: Error: no slot of name "queryHits" for this object of class "SortedByQueryHits" My workflow is basically, fo = findOverlaps(...) fo@queryHits Using queryHits(fo)