outputAnnotationResult,peakPantheRAnnotation-method {peakPantheR} | R Documentation |
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)
## S4 method for signature 'peakPantheRAnnotation' outputAnnotationResult( object, saveFolder, annotationName = "annotationResult", verbose = TRUE )
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 |
None
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) }