Description Usage Arguments Details Value Author(s) References Examples

View source: R/ScoringMatrix.R

These functions calculate the mutation matrix or Dayhoff matrix from the mutation matrix at PAM 1 and base backrgound frequency.

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`PAM1` |
A matrix of numeric: the mutation probability from one AA to another AA at PAM distance 1. The order of AA in the matrix should be identical to AACharacterSet. |

`n` |
A numeric: the PAM distance. |

`BF` |
A numeric vector: the backrgound frequency of AAs. The order of AA in the vector should also be identical to AACharacterSet. |

Calculate the n-PAM matrices from PAM1 mutation matrix and n. To compute n-PAM matrices, we multiply the PAM1 matrix through itself N times, which is most efficiently achieved through n additions in log space.

Computing Dayhoff matrices from PAM mutation matrices and AA frequency. Dayhoff matrices are the ratios P("alignment i and j arose through evolution") / P("alignment i and j arose by chance")

A numeric matrix is returned.

Ge Tan

Dayhoff, M.O., and Schwartz, R.M. (1978). A model of evolutionary change in proteins. In In Atlas of Protein Sequence and Structure,.

Gonnet, G.H., and Scholl, R. (2009). Scientific Computation (Cambridge, UK; New York: Cambridge University Press).

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