findPeakWidth: generic method findPeakWidth

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

Description

method findPeakWidth

Usage

findPeakWidth(
  object,
  p = 3,
  n = 5,
  span = 100,
  widthExtLower = 1.5,
  widthExtUpper = 1.75,
  ...
)

## S4 method for signature '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

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 'alsace'.

Value

object of class PeakList with 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))
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')

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