RMassBank (version 2.0.0)

reanalyzeFailpeaks: Reanalyze unmatched peaks

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

aggregated

A peake aggregate table (w@aggregate) (after processing electronic noise removal!)

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.

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.

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.

Details

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

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)