Description Usage Arguments Value Author(s) References See Also Examples

This function is a wrapper of `cwt`

, `getLocalMaximumCWT`

, `getRidge`

, `identifyMajorPeaks`

1 |

`ms` |
the mass spectrometry spectrum |

`scales` |
scales of CWT |

`SNR.Th` |
SNR (Signal to Noise Ratio) threshold |

`nearbyPeak` |
Determine whether to include the nearby small peaks of major peaks. TRUE by default |

`peakScaleRange` |
the scale range of the peak. larger than 5 by default. |

`amp.Th` |
the minimum required relative amplitude of the peak (ratio to the maximum of CWT coefficients) |

`minNoiseLevel` |
the minimum noise level used in computing the SNR |

`ridgeLength` |
the minimum highest scale of the peak in 2-D CWT coefficient matrix |

`peakThr` |
Minimal absolute intensity (above the baseline) of peaks to be picked. If this value is provided, then the smoothing function |

`tuneIn` |
determine whether to tune in the parameter estimation of the detected peaks |

`...` |
other parameters used by |

`majorPeakInfo` |
return of |

`ridgeList` |
return of |

`localMax` |
return of |

`wCoefs` |
2-D CWT coefficient matrix, see |

Pan Du, Simon Lin

Du, P., Kibbe, W.A. and Lin, S.M. (2006) Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching, Bioinformatics, 22, 2059-2065.

`cwt`

, `getLocalMaximumCWT`

, `getRidge`

, `identifyMajorPeaks`

1 2 3 4 5 6 7 8 9 10 11 12 | ```
data(exampleMS)
SNR.Th <- 3
peakInfo <- peakDetectionCWT(exampleMS, SNR.Th=SNR.Th)
majorPeakInfo = peakInfo$majorPeakInfo
peakIndex <- majorPeakInfo$peakIndex
plotPeak(exampleMS, peakIndex, main=paste('Identified peaks with SNR >', SNR.Th))
## In some cases, users may want to add peak filtering based on the absolute peak amplitude
peakInfo <- peakDetectionCWT(exampleMS, SNR.Th=SNR.Th, peakThr=500)
majorPeakInfo = peakInfo$majorPeakInfo
peakIndex <- majorPeakInfo$peakIndex
plotPeak(exampleMS, peakIndex, main=paste('Identified peaks with SNR >', SNR.Th))
``` |

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