Hi,
Our package - profileplyr - is failing on the development branch with an
error when it tries to subset a RangedSummarizedExperiment object with
brackets ([ ]). Within our package we build a slightly modified
RangedSummarizedExperiment object with a few additional slots and features,
and often will subset this object using the brackets in both the functions
and in the vignette. When trying to subset (e.g. object[1:10, 1:10]) we get
the error "Error: $ operator not defined for this S4 class". This is a new
error, so I wanted to check if this kind of subsetting functionality is no
longer supported with RangedSummarizedExperiment objects in general, or
whether this is likely something specific to our package. Any insight you
may have would be greatly appreciated - thanks!
Bestm
Doug
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