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. |