tofsims (version 1.0.2)

removePeaks: generic method removePeaks

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, ...)
## S3 method for class 'PeakList,missing,missing,numeric,missing':
removePeaks(object, mzs,
  operator, limit, nLocator, ...)
## S3 method for class 'PeakList,missing,missing,missing,numeric':
removePeaks(object, mzs,
  operator, limit, nLocator, ...)
## S3 method for class 'PeakList,numeric,missing,missing,missing':
removePeaks(object, mzs,
  operator, limit, nLocator, ...)
## S3 method for class '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')