# Preprocessing of FIA-HRMS data

## Documentation for package ‘proFIA’ version 1.13.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.