EICs accessor

EICs accessor

# S4 method for 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()
}
#> [[1]]
#> list()
#> 
#> [[2]]
#> list()
#> 
#> [[3]]
#> list()
#>