reanalyzeFailpeaks: Reanalyze unmatched peaks

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

View source: R/leMsMs.r

Description

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

Usage

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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

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## 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.