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
.Reset a peakPantheRAnnotation and alter samples and compounds information
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 peakPantheRAnnotation
resetAnnotation(previousAnnotation,
spectraPaths = NULL, targetFeatTable = NULL, uROI = NULL, FIR = NULL,
cpdMetadata = NULL, spectraMetadata = NULL, uROIExist = NULL,
useUROI = NULL, useFIR = NULL, verbose = TRUE, ...)
(peakPantheRAnnotation) object to reset
NULL or a character vector of spectra file paths, to set samples to process
NULL or a data.frame
of compounds to target as rows and parameters as columns: cpdID
(str), cpdName
(str), rtMin
(float in seconds), rt
(float in seconds, or NA), rtMax
(float in seconds), mzMin
(float), mz
(float or NA), mzMax
(float). Set compounds to target.
NULL or a data.frame of updated Regions Of Interest (uROI) with compounds as row and uROI parameters as columns: rtMin
(float in seconds), rt
(float in seconds, or NA), rtMax
(float in seconds), mzMin
(float), mz
(float or NA), mzMax
(float).
NULL or a data.frame of Fallback Integration Regions (FIR) with compounds as row and FIR parameters as columns: rtMin
(float in seconds), rtMax
(float in seconds), mzMin
(float), mzMax
(float).
NULL or a data.frame of compound metadata, with compounds as row and metadata as columns
NULL or a data.frame of sample metadata, with samples as row and metadata as columns
NULL or a logical stating if uROI have been set
NULL or a logical stating if uROI are to be used
NULL or a logical stating if FIR are to be used
(bool) If TRUE message progress
Additional slots and values to set when resetting the object (cpdID
, cpdName
, ROI
, filepath
, TIC
, acquisitionTime
, peakTables
, dataPoints
, peakFit
)
(peakPantheRAnnotation) object reset with previous results removed and slots updated