PeakList: Class PeakList

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

Description

Class PeakList is an extension of TIC class that can hold information about peaks.

Class PeakList inherits from the classes MassAnalysis, MassSpectra and TIC.

PeakList class constructor

Usage

PeakList(
  analysisName = NULL,
  instrument = NULL,
  nz = NULL,
  calibration = NULL,
  calibPoints = NULL,
  mz = NULL,
  peakIDs = NULL,
  peakMzs = NULL,
  ...
)

PeakList(
  analysisName = NULL,
  instrument = NULL,
  nz = NULL,
  calibration = NULL,
  calibPoints = NULL,
  mz = NULL,
  peakIDs = NULL,
  peakMzs = NULL,
  ...
)

Arguments

analysisName	character vector with the import filename
instrument	character vector type of instrument used in the experiment
nz	matrix numeric containing ion counts, rows are image points, column toftimes/mass to charge ratios
calibration	data frame for numerics slope and intercept of the mass calibration
calibPoints	data frame for time of flight to maass to charge calibration
mz	vector same length as columns in nz for mass to charge values
peakIDs	matrix integer ID for peaks
peakMzs	matrix with mass to charge values for lower, middle and upper peak values
...	additional args

Details

The PeakList class constructor is used to construct a new PeakList object. Input are currently all needed variables.

Value

object of class PeakList

Slots

peakIDs

matrix integer ID for peaks

peakMzs

matrix with mass to charge values for lower, middle and upper peak values

Author(s)

Lorenz Gerber <[e-mail]>

Lorenz Gerber <[e-mail]>

Examples

# The typical way to obtain a PeakList object is by
# applying some peak picking method to a MassSpectra
# below an example using the 'unitMassPeaks' method
library(tofsimsData)
data(tofsimsData)
testSpectra<-calibPointNew(testSpectra, mz = 15, value = 15.01551)
testSpectra<-calibPointNew(testSpectra, mz = 181, value = 181.0228)
testSpectra<-recalibrate(testSpectra)
testSpectra<-unitMassPeaks(testSpectra, mzRange = c(1,200), widthAt = c(15, 181), 
factor = c(0.4, 0.6), lower = c(14.97, 15.05), upper = c(180.84, 181.43))
show(testSpectra)

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