removePeaks: generic method removePeaks

In tofsims: Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data

Description

generic method removePeaks

removePeaks for PeakList Class allows removing peaks below a certain treshhold of ioncounts. the threshhold is not calculated as area, but just from the peak height (ion count at peak center)

removePeaks for PeakList Class allows removing peaks manually

removePeaks for PeakList Class allows removing peaks manually

Usage

removePeaks(object, mzs, operator, limit, nLocator, ...)

## S4 method for signature 'PeakList,missing,missing,numeric,missing'
removePeaks(object, mzs, operator, limit, nLocator, ...)

## S4 method for signature 'PeakList,missing,missing,missing,numeric'
removePeaks(object, mzs, operator, limit, nLocator, ...)

## S4 method for signature 'PeakList,numeric,missing,missing,missing'
removePeaks(object, mzs, operator, limit, nLocator, ...)

## S4 method for signature 'PeakList,missing,character,numeric,missing'
removePeaks(object, mzs, operator, limit, nLocator, ...)

Arguments

object	object of class PeakList
mzs	M/z's of peaks to be removed
operator	Accept ">", "<", "==", "<=", ">=", "!="
limit	numeric limit for peaks to be removed
nLocator	numeric how many peaks to remove with visual selection
...	additional args

Value

object of class PeakList with removed/updated peaks

Examples

library(tofsimsData)
data(tofsimsData)
testPeakList<-PeakList(analysisName = analysisName(testSpectra),
instrument = instrument(testSpectra),
nz = nz(testSpectra),
calibration = calibration(testSpectra),
calibPoints = calibPoints(testSpectra),
mz = mz(testSpectra),
peakIDs = NULL,
peakMzs = NULL)
par(mfcol=c(1,2))
testPeakList<-addPeaks(testPeakList, mzs = 26:31, width=0.4)
plot(testPeakList, mzRange = c(25,32), type = 'l')
testPeakList<-removePeaks(testPeakList, mzs = 27)
plot(testPeakList, mzRange = c(25,32), type = 'l')

tofsims documentation built on Nov. 8, 2020, 5:10 p.m.