peakTables-peakPantheRAnnotation-method: peakTables accessor with cpdID and cpdName added back

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

peakTables accessor with cpdID and cpdName added back

Description

peakTables accessor with cpdID and cpdName added back

Usage

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

Arguments

object

peakPantheRAnnotation

Value

(data.frame) A list of peakTable data.frame, of length number of spectra files. Each peakTable data.frame has compounds as rows and peak annotation results as columns, with added compound ID and name.

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

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