combineMultiplicities: Combine workspaces for multiplicity filtering

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

Description

Combines multiple msmsWorkspace items to one workspace which is used for multiplicity filtering.

Usage

combineMultiplicities(workspaces)

Arguments

workspaces

A vector of msmsWorkspace items. The first item is taken as the "authoritative" workspace, i.e. the one which will be used for the record generation. The subsequent workspaces will only be used for multiplicity filtering.

Details

This feature is particularily meant to be used in conjunction with the confirmMode option of msmsWorkflow: a file can be analyzed with confirmMode = 0 (default) and subsequently with confirmMode = 1 (take second highest scan). The second analysis should contain "the same" spectra as the first one (but less intense) and can be used to confirm the peaks in the first spectra.

TO DO: Enable the combination of workspaces for combining e.g. multiple energy settings measured separately.

Value

A msmsWorkspace object prepared for step 8 processing.

Author(s)

Stravs MA, Eawag <[e-mail]>

See Also

msmsWorkspace-class

Examples

## Not run: 
	w <- newMsmsWorkspace
 w@files <- c("spec1", "spec2")
 w1 <- msmsWorkflow(w, steps=c(1:7), mode="pH")
 w2 <- msmsWorkflow(w, steps=c(1:7), mode="pH", confirmMode = 1)
 wTotal <- combineMultiplicities(c(w1, w2))
 wTotal <- msmsWorkflow(wTotal, steps=8, mode="pH", archivename = "output")
 # continue here with mbWorkflow 

## End(Not run)

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