EICs-peakPantheRAnnotation-method: EICs accessor

In phenomecentre/peakPantheR: Peak Picking and Annotation of High Resolution Experiments

EICs accessor

Description

EICs accessor

Usage

## 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

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()
}

phenomecentre/peakPantheR documentation built on Feb. 29, 2024, 9:07 p.m.