reanalyzeFailpeaks: Reanalyze unmatched peaks
In RMassBank: Workflow to process tandem MS files and build MassBank records

Description Usage Arguments Details Value Author(s) See Also Examples

Reanalysis of peaks with no matching molecular formula by allowing additional elements (e.g. "N2O").

reanalyzeFailpeaks(aggregated, custom_additions, mode, filterSettings =
				getOption("RMassBank")$filterSettings, progressbar = "progressBarHook")
reanalyzeFailpeak(custom_additions, mass, cpdID, counter, pb = NULL, mode,
				filterSettings = getOption("RMassBank")$filterSettings)

`custom_additions`	The allowed additions, e.g. "N2O".
`mode`	Processing mode (`"pH", "pNa", "mH"` etc.)
`filterSettings`	Settings for filtering data. Refer to`analyzeMsMs` for settings.
`progressbar`	The progress bar callback to use. Only needed for specialized applications. Cf. the documentation of `progressBarHook` for usage.
`aggregated`	A peake aggregate table (`w@aggregate`) (after processing electronic noise removal!)
`mass`	(Usually recalibrated) m/z value of the peak.
`cpdID`	Compound ID of this spectrum.
`counter`	Current peak index (used exclusively for the progress indicator)
`pb`	A progressbar object to display progress on, as passed by `reanalyzeFailpeaks` to `reanalyzeFailpeak`. No progress is displayed if NULL.

reanalyzeFailpeaks examines the unmatchedPeaksC table in specs and sends every peak through reanalyzeFailpeak.

The aggregate data frame extended by the columns: #'

`reanalyzed.???`	If reanalysis (step 7) has already been processed: matching values from the reanalyzed peaks
`matchedReanalysis`	Whether reanalysis has matched (`TRUE`), not matched(`FALSE`) or has not been conducted for the peak(`NA`).

It would be good to merge the analysis functions of analyzeMsMs with the one used here, to simplify code changes.

Michael Stravs

analyzeMsMs, msmsWorkflow

## As used in the workflow:
## Not run:     
	reanalyzedRcSpecs <- reanalyzeFailpeaks(w@aggregated, custom_additions="N2O", mode="pH")
# A single peak:
reanalyzeFailpeak("N2O", 105.0447, 1234, 1, 1, "pH")

## End(Not run)