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

Description Usage Arguments Value Examples

Description

peakTables accessor with cpdID and cpdName added back

Usage

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## 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

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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
}

peakPantheR documentation built on April 29, 2020, 5:23 a.m.