resetAnnotation,peakPantheRAnnotation-method {peakPantheR} | R Documentation |
Reset a peakPantheRAnnotation (remove results and set
isAnnotated=FALSE
). If a different number of samples (
spectraPaths
) or compounds (targetFeatTable
) are passed, the
object will be initialised to the new size. For input values left as NULL,
the slots (filepath
(from spectraPaths
), ROI
,
cpdID
, cpdName
(from targetFeatTable
), uROI
,
FIR
, cpdMetadata
, spectraMetadata
, uROIExist
,
useUROI
and useFIR
) will be filled with values from
previousAnnotation
.
## S4 method for signature 'peakPantheRAnnotation' resetAnnotation( previousAnnotation, spectraPaths = NULL, targetFeatTable = NULL, uROI = NULL, FIR = NULL, cpdMetadata = NULL, spectraMetadata = NULL, uROIExist = NULL, useUROI = NULL, useFIR = NULL, verbose = TRUE, ... )
previousAnnotation |
(peakPantheRAnnotation) object to reset |
spectraPaths |
NULL or a character vector of spectra file paths, to set samples to process |
targetFeatTable |
NULL or a |
uROI |
NULL or a data.frame of updated Regions Of Interest (uROI) with
compounds as row and uROI parameters as columns: |
FIR |
NULL or a data.frame of Fallback Integration Regions (FIR) with
compounds as row and FIR parameters as columns: |
cpdMetadata |
NULL or a data.frame of compound metadata, with compounds as row and metadata as columns |
spectraMetadata |
NULL or a data.frame of sample metadata, with samples as row and metadata as columns |
uROIExist |
NULL or a logical stating if uROI have been set |
useUROI |
NULL or a logical stating if uROI are to be used |
useFIR |
NULL or a logical stating if FIR are to be used |
verbose |
(bool) If TRUE message progress |
... |
Additional slots and values to set when resetting the object
( |
(peakPantheRAnnotation) object reset with previous results removed and slots updated
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')) # 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)) smallAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths, targetFeatTable=targetFeatTable) smallAnnotation # An object of class peakPantheRAnnotation # 2 compounds in 2 samples. # updated ROI do not exist (uROI) # does not use updated ROI (uROI) # does not use fallback integration regions (FIR) # is not annotated # Reset and change number of spectra newSpectraPaths <- 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')) largerAnnotation <- resetAnnotation(smallAnnotation, spectraPaths=newSpectraPaths, verbose=TRUE) largerAnnotation # An object of class peakPantheRAnnotation # 2 compounds in 3 samples. # updated ROI do not exist (uROI) # does not use updated ROI (uROI) # does not use fallback integration regions (FIR) # is not annotated }