Dynamic programming based alignment of MS2 chromatograms

calcNoBeefMaskGlobal | Hard constraining of similarity matrix outside of global fit... |

calcNoBeefMaskGlobalWSlope | Soft constraining of similarity matrix outside of global fit... |

constrainSimilarity | Hard constraining of similarity matrix outside of global fit... |

getAffineAlignObj | Creates affine alignment object |

getAlignment | Computes indices of row and column of maximum scored... |

getAlignmentPath | Output matrix with alignment path represented as binary-hot... |

getGapPenalty | Calculates gap penalty |

getLinearfit | calculates linear fit between RT of two runs |

getLOESSfit | calculates LOESS fit between RT of two runs |

getSimilarityMatrix | calculates similarity matrix between two chromatogram groups |

mapIdxToTime | Establishes mapping back from index to time |

NeedleObjAffine-class | An S4 object to group matrices produced by the alignmnet |

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