filterMultiplicity: filterMultiplicity

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

Description

Multiplicity filtering: Removes peaks which occur only once in a n-spectra set.

Usage

filterMultiplicity(w, archivename=NA, mode="pH", recalcBest = TRUE,
		multiplicityFilter = getOption("RMassBank")$multiplicityFilter)

Arguments

w	Workspace containing the data to be processed (aggregate table and RmbSpectraSet objects)
archivename	The archive name, used for generation of archivename_Failpeaks.csv
mode	Mode of ion analysis
recalcBest	Boolean, whether to recalculate the formula multiplicity after the first multiplicity filtering step. Sometimes, setting this to FALSE can be a solution if you have many compounds with e.g. fluorine atoms, which often have multiple assigned formulas per peak and might occasionally lose peaks because of that.
multiplicityFilter	Threshold for the multiplicity filter. If set to 1, no filtering will apply (minimum 1 occurrence of peak). 2 equals minimum 2 occurrences etc.

Details

This function executes multiplicity filtering for a set of spectra using the workhorse function filterPeaksMultiplicity (see details there) and retrieves problematic filtered peaks (peaks which are of high intensity but were discarded, because either no formula was assigned or it was not present at least 2x), using the workhorse function problematicPeaks. The results are returned in a format ready for further processing with mbWorkflow.

Value

A list object with values:

peaksOK	Peaks with >1-fold formula multiplicity from the "normal" peak analysis.
peaksReanOK	Peaks with >1-fold formula multiplicity from peak reanalysis.
peaksFiltered	All peaks with annotated formula multiplicity from first analysis.
peaksFilteredReanalysis	All peaks with annotated formula multiplicity from peak reanalysis.
peaksProblematic	Peaks with high intensity which do not match inclusion criteria -> possible false negatives. The list will be exported into archivename_failpeaks.csv.

Author(s)

Michael Stravs

See Also

filterPeaksMultiplicity,problematicPeaks

Examples

## Not run: 
    refilteredRcSpecs <- filterMultiplicity(
			w, "myarchive", "pH")

## End(Not run)

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