EICs,peakPantheRAnnotation-method {peakPantheR} | R Documentation |
EICs accessor
## S4 method for signature 'peakPantheRAnnotation' EICs(object, aggregationFunction)
object |
peakPantheRAnnotation |
aggregationFunction |
(str) Function to use in order to aggregate
intensities across mz in each scan. One of |
(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() }