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