EICs accessor
# S4 method for peakPantheRAnnotation
EICs(object, aggregationFunction)
peakPantheRAnnotation
(str) Function to use in order to aggregate
intensities across mz in each scan. One of sum
, max
,
min
, mean
(float) Extracted Ion Chromatogram aggregated across mz in each scan
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()
#>