Preprocessing of FIA-HRMS data

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Documentation for package ‘proFIA’ version 1.8.0

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proFIA-package Process FIA-HRMS datasets.
acquisitionDirectory Ge the class organization of directory.
analyzeAcquisitionFIA Wrapper function for the full FIA analysis workflow.
dataMatrix An S4 class to represent an FIA experiments.
dataMatrix-method An S4 class to represent an FIA experiments.
determiningInjectionZone First guess of the limit of the injection peak.
determiningSizePeak Determine the limits of the injection peak in a FIA acquisition.
determiningSizePeak.Geom Determine the limits of the injection peak in a FIA acquisition.
estimateNoiseMS Estimate the noise of a mass spectrometer using multiple MS acquisition.
exportDataMatrix Export data matrix.
exportDataMatrix-method Export data matrix.
exportExpressionSet Export proFIAset to ExpressionSet
exportExpressionSet-method Export proFIAset to ExpressionSet
exportPeakTable Export proFIAset as a peak table.
exportPeakTable-method Export proFIAset as a peak table.
exportSampleMetadata Export samples metadata.
exportSampleMetadata-method Export samples metadata.
exportVariableMetadata Export variable metadata.
exportVariableMetadata-method Export variable metadata.
findBandsFIA Detect band in a FIA acquisition
findFIASignal Detect peaks in an FIA acquisition.
findMzGroup find a group in a FIA experiment.
findMzGroup-method find a group in a FIA experiment.
findPeaks Detect peaks in an FIA acquisition.
getInjectionPeak Fit an injection peak to an FIA acquisition.
group.FIA Group the peaks of an FIA acquisition.
group.FIA-method Group the peaks of an FIA acquisition.
groupMatrix An S4 class to represent an FIA experiments.
groupMatrix-method An S4 class to represent an FIA experiments.
impute.FIA Fill missing values using the provided method.
impute.FIA-method Fill missing values using the provided method.
impute.KNN_TN Fill missing values in the peak table using K-nearest Neighbour for tuncated distributions.
impute.KNN_TN-method Fill missing values in the peak table using K-nearest Neighbour for tuncated distributions.
impute.randomForest Fill missing values in the peak table using random forest.
impute.randomForest-method Fill missing values in the peak table using random forest.
injectionPeaks An S4 class to represent an FIA experiments.
injectionPeaks-method An S4 class to represent an FIA experiments.
makeDataMatrix Construct the data matrix of a proFIAset object.
makeDataMatrix-method Construct the data matrix of a proFIAset object.
noiseEstimation-class An S4 class to represent heteroscedasctic noise of MS.
peaks An S4 class to represent an FIA experiments.
peaks-method An S4 class to represent an FIA experiments.
peaksGroup Return the peaks corresponding to a group.
peaksGroup-method Return the peaks corresponding to a group.
phenoClasses An S4 class to represent an FIA experiments.
phenoClasses-method An S4 class to represent an FIA experiments.
plot-method Plot a summary of an FIA experiment.
plot.FIA Plot a summary of an FIA experiment.
plotFlowgrams Plot raw temporal profiles of the selected group.
plotFlowgrams-method Plot raw temporal profiles of the selected group.
plotNoise Plot the estimated noise from a proFIAset object.
plotRaw Plotting of raw data
plotRaw-method Plotting of raw data
plotSamplePeaks Plot the sample peak of a proFIAset object.
plotSamplePeaks-method Plot the sample peak of a proFIAset object.
proFIA Process FIA-HRMS datasets.
proFIAset Process FIA experiment.
proFIAset-class An S4 class to represent an FIA experiments.