dataPoints-peakPantheRAnnotation-method: dataPoints accessor

In phenomecentre/peakPantheR: Peak Picking and Annotation of High Resolution Experiments

dataPoints accessor

Description

dataPoints accessor

Usage

## S4 method for signature 'peakPantheRAnnotation'
dataPoints(object)

Arguments

object

peakPantheRAnnotation

Value

A list of length number of spectra files. Each list element is a ROIsDataPoint list of data.frame of raw data points for each ROI/uROI (retention time 'rt', mass 'mz' and intensity 'int' (as column) of each raw data points (as row))

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
dataPoints(annotation)
# [[1]]
# NULL
# [[2]]
# NULL
# [[3]]
# NULL
}

phenomecentre/peakPantheR documentation built on Feb. 29, 2024, 9:07 p.m.