annotationTable-peakPantheRAnnotation-method: annotationTable accessor

Description Usage Arguments Value Examples

Description

annotationTable returns a dataframe (row samples, col compounds) filled with a specific peakTable column

Usage

1
2
## S4 method for signature 'peakPantheRAnnotation'
annotationTable(object, column)

Arguments

object

peakPantheRAnnotation

column

a peakTable columns

Value

(data.frame) (row samples, col compounds) filled with a specific peakTable column

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
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
annotationTable(annotation)
#                                             ID-1 ID-2
# C:/R/R-3.6.0/library/faahKO/cdf/KO/ko15.CDF   NA   NA
# C:/R/R-3.6.0/library/faahKO/cdf/KO/ko16.CDF   NA   NA
# C:/R/R-3.6.0/library/faahKO/cdf/KO/ko18.CDF   NA   NA
}

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