outputAnnotationResult-peakPantheRAnnotation-method: Save to disk all annotation results as csv files

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

Save to disk all annotation results as csv files

Description

Save to disk all annotation results as annotationName_ ... .csv files: compound metadata (cpdMetadata, cpdID, cpdName) and spectra metadata (spectraMetadata, acquisitionTime, TIC), summary of fit (ratio of peaks found: ratio_peaks_found, ratio of peaks filled: ratio_peaks_filled, mean ppm_error: ppm_error, mean rt_dev_sec: rt_dev_sec), and a file for each column of peakTables (with samples as rows and compounds as columns)

Usage

## S4 method for signature 'peakPantheRAnnotation'
outputAnnotationResult(
    object,
    saveFolder,
    annotationName = "annotationResult",
    verbose = TRUE
)

Arguments

object	(peakPantheRAnnotation) Annotated peakPantheRAnnotation object
saveFolder	(str) Path of folder where the annotation result csv will be saved
annotationName	(str) name of annotation to use in the saved csv
verbose	(bool) If TRUE message progress

Value

None

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))

emptyAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
                                        targetFeatTable=targetFeatTable)

# Calculate annotation
annotation      <- peakPantheR_parallelAnnotation(emptyAnnotation, ncores=0,
                                getAcquTime=FALSE, verbose=FALSE)$annotation

# temporary location
savePath1       <- tempdir()
outputAnnotationResult(annotation, saveFolder=savePath1,
                        annotationName='testProject', verbose=TRUE)
}

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