Disengagement score is defined as
A pseudo-count of one is added to both the ORF and downstream sums.
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RiboSeq reads as GAlignments, GRanges or GRangesList object
If it is
logical (FALSE), an optimizer, have you ran this line:
a vector (default: 1L, if 1L it is identical to countOverlaps()), if single number (!= 1), it applies for all, if more than one must be equal size of 'reads'. else it must be the string name of a defined meta column in subject "reads", that gives number of times a read was found. GRanges("chr1", 1, "+", score = 5), would mean "score" column tells that this alignment region was found 5 times.
an integer, (default: NULL), if defined must be countOverlaps(grl, RFP), added for speed if you already have it
a named vector of numeric values of scores
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