Generate ion chromatogram from raw data points
peakFit,peakPantheRAnnotation-method
peakFit accessor
Check if object is of class peakPantheR_curveFit
outputAnnotationResult,peakPantheRAnnotation-method
Save to disk all annotation results as csv files
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)
Plot variable histogram and density
resetAnnotation,peakPantheRAnnotation-method
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
.
Predict curve values
Plot peak value and peakwidth by acquisition time or in input order
Plot samples raw data and detected feature for a single ROI
skewedGaussian_minpack.lm
Implementation of the Skewed Gaussian peak shape for use with minpack.lm
Plot samples raw data and detected feature for a single ROI
isAnnotated,peakPantheRAnnotation-method
isAnnotated accessor
Guess function for initial skewed gaussian parameters and bounds
spectraMetadata,peakPantheRAnnotation-method
spectraMetadata accessor
skewedGaussian_minpack.lm_objectiveFun
Skewed Gaussian minpack.lm objective function
peakTables,peakPantheRAnnotation-method
peakTables accessor with cpdID and cpdName added back
peakPantheR_singleFileSearch
Search, integrate and report targeted features in a raw spectra
nbCompounds,peakPantheRAnnotation-method
nbCompounds accessor established on cpdID
nbSamples,peakPantheRAnnotation-method
nbSamples accessor established on filepath
Extract signal in a multiple defined mz rt window from a raw data file
peakPantheR: A package for Peak Picking and ANnoTation of High resolution Experiments
outputAnnotationParamsCSV,peakPantheRAnnotation-method
Save annotation parameters as CSV
Save annotation parameters (ROI, uROI and FIR) to disk as a CSV file for editing
outputAnnotationDiagnostic,peakPantheRAnnotation-method
Save to disk the annotation parameters as CSV and a diagnostic plot per fitted compound
Save to disk the annotation parameters as CSV (as generated by outputAnnotationParamsCSV()
) and a diagnostic plot per fitted compound (as generated by annotationDiagnosticMultiplot()
) if savePlots
is TRUE
[,peakPantheRAnnotation,ANY,ANY,ANY-method
extract parts of peakPantheRAnnotation class
uROI,peakPantheRAnnotation-method
uROI accessor returns targetFeatTable with cpdID, cpdName added
getTargetFeatureStatistic
Calculate chromatographic peak properties
Integrate fallback integration regions
peakPantheR_parallelAnnotation
Search, integrate and report targeted features in a multiple spectra
peakPantheR_loadAnnotationParamsCSV
Load fit parameters from CSV
An S4 class to represent peakPantheR annotation results
Save to disk a plot of all ROI EIC and detected feature range
uROIExist,peakPantheRAnnotation-method
uROIExist accessor
useUROI,peakPantheRAnnotation-method
useUROI accessor
useFIR,peakPantheRAnnotation-method
useFIR accessor
Gaussian Error function
annotationTable,peakPantheRAnnotation-method
annotationTable accessor
annotationTable returns a dataframe (row samples, col compounds) filled with a specific peakTable column
cpdID,peakPantheRAnnotation-method
cpdID accessor
cpdName,peakPantheRAnnotation-method
cpdName accessor
EICs,peakPantheRAnnotation-method
EICs accessor
cpdMetadata,peakPantheRAnnotation-method
cpdMetadata accessor
ROI,peakPantheRAnnotation-method
ROI accessor returns targetFeatTable with cpdID, cpdName added
FIR,peakPantheRAnnotation-method
FIR accessor returns targetFeatTable with cpdID, cpdName added
annotationDiagnosticPlots,peakPantheRAnnotation-method
Generate fit diagnostic plots
Generate fit diagnostic plots for each ROI: EICFit
the raw data and detected feature fit, rtPeakwidthVert
detected peaks retention time apex and peakwidth (vertical and no run order), rtPeakwidthHorzRunOrder
detected peaks retention time apex and peakwidth by run order, mzPeakwidthHorzRunOrder
detected peaks m/z apex and peakwidth by run order, areaRunOrder
detected peaks area by run order, rtHistogram
histogram of detected peaks retention time, mzHistogram
histogram of detected peaks m/z, areaHistogram
histogram of detected peaks area.
TIC,peakPantheRAnnotation-method
TIC accessor
filename,peakPantheRAnnotation-method
filename accessor by spliting filepath
Parse acquisition date from a mzML file
acquisitionTime,peakPantheRAnnotation-method
acquisitionTime accessor returns value as.POSIXct
filepath,peakPantheRAnnotation-method
filepath accessor
annotationDiagnosticMultiplot
Generate a multiplot of all diagnostic plots
dataPoints,peakPantheRAnnotation-method
dataPoints accessor
annotationParamsDiagnostic,peakPantheRAnnotation-method
Set uROI and FIR based on annotation results
Set updated ROI (uROI) and Fallback Integration Regions (FIR) based on the annotation results. If the object is not annotated, it is returned untouched. ROI is not modified. If uROI exist they are left untouched, otherwise they are set as the minimum and maximum found peaks limits (+/-5% of ROI in retention time). If FIR are used they are left untouched, otherwise they are set as the median of the found limits (rtMin, rtMax, mzMin, mzMax).
Find and integrate target features in each ROI
Curve fitting using minpack.lm