Preprocessing of FIA-HRMS data


[Up] [Top]

Documentation for package ‘proFIA’ version 1.0.10

Help Pages

proFIA-package Process FIA-HRMS datasets.
acquisitionDirectory Create a table containg the classes of the acquisition.
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.
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.
estimateNoiseListFiles Estimate the noise of 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.
fillPeaks.WKNN Fill missing values in the peak table.
fillPeaks.WKNN-method Fill missing values in the peak table.
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.
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.
plotEICs Plot raw temporal profiles of the selected group.
plotEICs-method Plot raw temporal profiles of the selected group.
plotInjectionPeaks Plot the injection peaks of a proFIAset object.
plotInjectionPeaks-method Plot the injection peaks of a proFIAset object.
plotNoise Plot the estimated noise from a proFIAset object.
plotRaw plotting of raw data
plotRaw-method plotting of raw data
proFIA Process FIA-HRMS datasets.
proFIAset Process FIA experiment.
proFIAset-class An S4 class to represent an FIA experiments.