FIR,peakPantheRAnnotation-method {peakPantheR} | R Documentation |
FIR accessor returns targetFeatTable with cpdID, cpdName added
## S4 method for signature 'peakPantheRAnnotation' FIR(object)
object |
peakPantheRAnnotation |
(data.frame) target feature table with compounds as row and FIR parameters as columns
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 FIR(annotation) # rtMin rtMax mzMin mzMax cpdID cpdName # 1 NA NA NA NA ID-1 Cpd 1 # 2 NA NA NA NA ID-2 Cpd 2 }