The granges,MethPat and granges,SparseMethPat object currently call rowRanges() (as of SummarizedExperiment 1.1.0 and SparseSummarizedExperimentf3a0e62). This means that the returned object is not strictly a GRanges object, since it will return a GTuples object in these cases. Should a patch be proposed to SummarizedExperiment so that granges(x) effectively calls granges(rowRanges(x))? Note that ?granges does point out that granges() is, somewhat unusually, both a "getter" and a "coercer".
There is a similar issue forgrglist(), although this does not seem to be currently used in the GenomicRanges or SummarizedExperiment packages.
The
granges,MethPatandgranges,SparseMethPatobject currently callrowRanges()(as of SummarizedExperiment 1.1.0 and SparseSummarizedExperiment f3a0e62). This means that the returned object is not strictly aGRangesobject, since it will return aGTuplesobject in these cases. Should a patch be proposed to SummarizedExperiment so thatgranges(x)effectively callsgranges(rowRanges(x))? Note that?grangesdoes point out thatgranges()is, somewhat unusually, both a "getter" and a "coercer".There is a similar issue for
grglist(), although this does not seem to be currently used in the GenomicRanges or SummarizedExperiment packages.