processingData slot is overwritten by initialize,MSnSet

[sgibb]

Currently initialize overwrites the processingData slot of MSnSet objects (inherit from pSet). Is that expected?

MSnbase/R/methods-MSnSet.R

Line 43 in 69d68e6

.Object@processingData <- new("MSnProcess")

That's why something like this is necessary:

MSnbase/R/quantitation-MS2-isobaric.R

Lines 58 to 67 in 69d68e6

	msnset <- new("MSnSet",
	qual = data.frame(.qual),
	exprs = .exprs,
	experimentData = experimentData(object),
	phenoData = .phenoData,
	featureData = .featureData,
	annotation = "No annotation")
	## copying processingData
	msnset@processingData <- object@processingData

IMHO the following should work:

new("MSnSet", processingData=new("MSnProcess", processing="Created"))

Is there any reason for overwriting the processingData slot?

[lgatto]

No, there isn't any good reason indeed, and a patch would be welcome.