PeakList: Class PeakList

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

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

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

Value

object of class PeakList

Details

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

Examples

Run this code

# 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)