I have thought about this and I actually think this should have a separate package instead of being incorporated into mzR or mzID. Both of these package are parsers and shouldn't come with so much else additional cruft, and certainly not depend on each other. It should be perfectly legal to only have mzID if the interest is only in evaluating search results...
I'm thinking a new package that defines how the two different objects work together would make sense, as there could also be standard plotting methods for the objects and combinations of the objects there; something that doesn't fit into a parser, but still general enough for a lot of people to want...
Anyway - this is just a start of a possibly long discussion on the subject, and as there is no code yet it is still a moot point : )
I have thought about this and I actually think this should have a separate package instead of being incorporated into mzR or mzID. Both of these package are parsers and shouldn't come with so much else additional cruft, and certainly not depend on each other. It should be perfectly legal to only have mzID if the interest is only in evaluating search results...
I'm thinking a new package that defines how the two different objects work together would make sense, as there could also be standard plotting methods for the objects and combinations of the objects there; something that doesn't fit into a parser, but still general enough for a lot of people to want...
Anyway - this is just a start of a possibly long discussion on the subject, and as there is no code yet it is still a moot point : )