EICs-peakPantheRAnnotation-method: EICs accessor

Description Usage Arguments Value Examples

Description

EICs accessor

Usage

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## S4 method for signature 'peakPantheRAnnotation'
EICs(object, aggregationFunction)

Arguments

object

peakPantheRAnnotation

aggregationFunction

(str) Function to use in order to aggregate intensities across mz in each scan. One of sum, max, min, mean

Value

(float) Extracted Ion Chromatogram aggregated across mz in each scan

Examples

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if(requireNamespace('faahKO')){
## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
## compounds

# Paths to spectra files
library(faahKO)
spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
                    system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
                    system.file('cdf/KO/ko18.CDF', package = 'faahKO'))

# targetFeatTable
targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
                    c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
                    'mzMax'))), stringsAsFactors=FALSE)
targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
                        522.2, 522.205222)
targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
                        496.2, 496.204962)
targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
                                    FUN.VALUE=numeric(2))

annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
                                    targetFeatTable=targetFeatTable)

## default values without annotation
EICs(annotation)
# [[1]]
# list()
# [[2]]
# list()
# [[3]]
# list()
}

peakPantheR documentation built on April 29, 2020, 5:23 a.m.