src/doc_pages/Initialization.md

In Roestlab/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

@subpage Initialization

We initialize M, A and B matrices for overlap alignment and non-overlap alignment. Aligning Ai with B0 without a gap. Not possible, hence, First column of M is initialized with -\f$\infty\f$. Aligning A0 with Bj without a gap. Not possible, hence, First row of M is initialized with -\f$\infty\f$. * M0,0 should have zero to begin the alignment using dynamic programming.

M | 0 | 1 | 2 | 3 | 4 | 5 | --|--|--|--|--|--|--- 0 | 0 | -\f$\infty\f$ | -\f$\infty\f$ | -\f$\infty\f$ | -\f$\infty\f$ | -\f$\infty\f$ | 1 | -\f$\infty\f$ | | | | | | 2 | -\f$\infty\f$ | | | | | | 3 | -\f$\infty\f$ | | | | | |

• Score of the best alignment between Ai and B0 that introduces a gap in A. Not possible, hence, First column of B is initialized with -\f$\infty\f$.
• Score of the best alignment between A0 and Bj that results a gap in B. Not possible, hence, First row of A is initialized with -\f$\infty\f$.

@section Init_section1 Overlap alignment

A | 0 | 1 | 2 | 3 | 4 | 5 | --|--|--|--|--|--|---| 0 | -\f$\infty\f$ | -\f$\infty\f$ | -\f$\infty\f$ | -\f$\infty\f$ | -\f$\infty\f$ | -\f$\infty\f$ | 1 | 0 | | | | | | 2 | 0 | | | | | | 3 | 0 | | | | | |

B | 0 | 1 | 2 | 3 | 4 | 5 | --|--|--|--|--|--|---| 0 | -\f$\infty\f$ | 0 | 0 | 0 | 0 | 0 | 1 | -\f$\infty\f$ | | | | | | 2 | -\f$\infty\f$ | | | | | | 3 | -\f$\infty\f$ | | | | | |

@section Init_section2 Non-overlap alignment

A | 0 | 1 | 2 | 3 | 4 | 5 | --|--|--|--|--|--|---| 0 | -\f$\infty\f$ | -\f$\infty\f$ | -\f$\infty\f$ | -\f$\infty\f$ | -\f$\infty\f$ | -\f$\infty\f$ | 1 | -22 | | | | | | 2 | -29 | | | | | | 3 | -36 | | | | | |

B | 0 | 1 | 2 | 3 | 4 | 5 | --|--|--|--|--|--|---| 0 | -\f$\infty\f$ | -22 | -29 | -36 | -43 | -50 | 1 | -\f$\infty\f$ | | | | | | 2 | -\f$\infty\f$ | | | | | | 3 | -\f$\infty\f$ | | | | | |

Roestlab/DIAlignR documentation built on March 3, 2021, 9:09 a.m.