reanalyzeFailpeaks: Reanalyze unmatched peaks

In sneumann/RMassBank: Workflow to process tandem MS files and build MassBank records

Description

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

Usage

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

Arguments

custom_additions	The allowed additions, e.g. "N2O".
mode	Processing mode ("pH", "pNa", "mH" etc.)
filterSettings	Settings for filtering data. Refer toanalyzeMsMs 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.

Details

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

Value

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.

Author(s)

Michael Stravs

See Also

analyzeMsMs, msmsWorkflow

Examples

## 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)

sneumann/RMassBank documentation built on Oct. 20, 2020, 3:19 p.m.