FIR-peakPantheRAnnotation-method: FIR accessor returns targetFeatTable with cpdID, cpdName...
In peakPantheR: Peak Picking and Annotation of High Resolution Experiments

Description Usage Arguments Value Examples

FIR accessor returns targetFeatTable with cpdID, cpdName added

1 2	## 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
}