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| Autotuner | Autotuner |
| Autotuner-class | Autotuner |
| checkBounds | checkBounds |
| checkEICPeaks | checkEICPeaks |
| createAutotuner | createAutotuner |
| dissectScans | dissectScans |
| EICparams | EICparams |
| eicParamsEsts | eicParamsEsts |
| estimatePPM | estimatePPM |
| estimateSNThresh | estimateSNThresh |
| extract_peaks | extract_peaks |
| filterPeaksfromNoise | filterPeaksfromNoise |
| filterPpmError | filterPpmError |
| findPeakWidth | findPeakWidth |
| findTruePeaks | findTruePeaks |
| getAutoFactorCol | getAutoFactorCol |
| getAutoFile_col | getAutoFile_col |
| getAutoFile_paths | getAutoFile_paths |
| getAutoIntensity | getAutoIntensity |
| getAutoMetadata | getAutoMetadata |
| getAutoPeaks | getAutoPeaks |
| getAutoPeak_difference | getAutoPeak_difference |
| getAutoPeak_table | getAutoPeak_table |
| getAutoTime | getAutoTime |
| initialize-method | Update an 'Autotuner' object |
| isolatePeaks | isolatePeaks |
| mzDb | mzDb |
| observedPeak | observedPeak |
| peakwidth_est | peakwidth_est |
| peakwidth_table | peakwidth_table |
| peak_time_difference | peak_time_difference |
| plot_peaks | @title plot_peaks |
| plot_signals | plot_signals |
| returnParams | returnParams |
| setAutoFactorCol | setAutoFactorCol |
| setAutoFile_col | setAutoFile_col |
| setAutoFile_paths | setAutoFile_paths |
| setAutoIntensity | setAutoIntensity |
| setAutoMetadata | setAutoMetadata |
| setAutoPeaks | setAutoPeaks |
| setAutoPeak_difference | setAutoPeak_difference |
| setAutoPeak_table | setAutoPeak_table |
| setAutoTime | setAutoTime |
| ThresholdingAlgo | ThresholdingAlgo |
| TIC_params | TIC_params |