Add some more Spectra methods

[jorainer]

Add filterMsLevel,Spectra, coerce,Spectra,list and coerce,Spectra,MSnExp (issue #370) and clean,Chromatograms (issue #354).

[sgibb]

Great!

[jorainer]

No change requests at all @sgibb ? for real?

[sgibb]

No, IMHO its fine. There is only a small point with the processing message for the MSnExp. We have a logging function in R/utils.R where we use "[", date(), "]" instead of date():

MSnbase/R/utils.R

Lines 619 to 626 in 367b26f

	logging <- function(object, msg, date. = TRUE) {
	if (date.)
	msg <- paste0(msg, " [", date(), "]")
	object@processingData@processing <-
	c(object@processingData@processing, msg)
	if (validObject(object))
	return(object)
	}

But I have seen that we don't be consistent here:

MSnbase/R/readMSData.R

Lines 89 to 90 in 367b26f

	process <- new("MSnProcess",
	processing = paste("No data loaded:", date()))

MSnbase/R/readMSData.R

Line 281 in 367b26f

processing = paste("Data loaded:", date()),

MSnbase/R/readMSnSet.R

Lines 23 to 24 in 70a9ec3

	processing=paste("Quantitation data loaded:",date(),
	" using readMSnSet."),

MSnbase/R/functions-MSnExp.R

Lines 66 to 69 in 57fb5db

	object@processingData@processing <- c(object@processingData@processing,
	paste(n," (",m,
	") precursors (spectra) extracted: ",
	date(),sep=""))

MSnbase/R/functions-MSnExp.R

Lines 88 to 92 in 57fb5db

	object@processingData@processing <- c(object@processingData@processing,
	paste("Curves <= ",
	t
	," set to '0': ",
	date(),sep=""))

In fact we more often use the date() construct than "[", date(), "]" or logging:

$ grep -o "date()" *.R | wc -l
45
$ grep -o "logging(" *.R | wc -l
27

So I wasn't sure what to do and didn't mention it.

[jorainer]

I wasn't even aware of the "[", date(), "]" - I used readMSData as template.

[lgatto]

Why aren't all feature variables passed along during coercion? I would prefer to keep all of them by default and have a selectFeatureData function to select those to keep.

[sgibb]

I guessed because they are part of a Spectrum object?

[jorainer]

I did not pass all feature variables to avoid redundancy. All these that are not passed along will be present (are set) in the individual Spectrum object - so no need to have them in addition as metadata columns.

[lgatto]

Indeed, thank you. Is there already an accessor for these (centroided,Spectra, ...)? The implementation will be identical to the corresponding in memory MSnExp methods.

[jorainer]

Yes, all methods to access slot values for Spectrum objects are also implemented for Spectra objects (in methods-Spectra.R), returning always a vector of length equal to Spectra with the corresponding slot values.