tofsims (version 1.0.2)

findPeakWidth: generic method findPeakWidth

Description

generic method findPeakWidth

method findPeakWidth

Usage

findPeakWidth(object, p = 3, n = 5, span = 100, widthExtLower = 1.5,
  widthExtUpper = 1.75, ...)
## S3 method for class 'PeakList':
findPeakWidth(object, p = 3, n = 199, span = 100,
  widthExtLower = 1.7, widthExtUpper = 2, ...)

Arguments

object

object of class PeakList

p

numeric value for savitzky-golay filter on first derivate

n

numeric value for savitzky-golay filter on first derivate

span

numeric smoothing for determining local minima/maxima values

widthExtLower

numeric factor to extend lower peak width

widthExtUpper

numeric factor to extend upper peak width

...

additional args

Value

• object of class PeakList with updated peaks

Details

This method uses signal processing to determine lower and upper peak width limits based on local max/min detection of the first derivate next to peak center values. The initial code for local min/max detection is adapted from the CRAN package 'ChemometricsWithR'.

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))
plot(testPeakList, mzRange=c(25,32), type = 'l')
testPeakList<-addPeaks(testPeakList, mzs=26:31, width=0.4)
testPeakList<-findPeakWidth(testPeakList, p = 3, n = 199, 
span = 100, widthExtLower = 2, widthExtUpper = 2)
plot(testPeakList, mzRange=c(25,32), type = 'l')