PeakList: Class PeakList

Description Usage Arguments Details Value Slots Author(s) Examples

View source: R/PeakList.R

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

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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 <lorenz.gerber@slu.se>

Lorenz Gerber <lorenz.gerber@slu.se>

Examples

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# 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 May 20, 2017, 10:45 p.m.

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