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

Perform the Smith-Waterman algorithm on a vector of real values.

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`x` |
a vector of real values |

`max.nIslands` |
the number of iterations of the algorithm performed. Each iteration finds the next highest-scoring 'island' of positive values. Set to NULL to find all islands |

`trace` |
print verbose output if TRUE |

The Smith-Waterman algorithm detects 'islands' of positive scores in a vector of
real values. The input values should have a negative mean. The algorithm can be
used to identify regions of copy number change in microarray fluorescence
logratios, once the logratios have been adjusted for sign and a suitable
threshold value subtracted to ensure a negative mean: see `sw.threshold`

`x` |
the input vector |

`s` |
a numeric vector containing the partial sums after one iteration of the Smith-Waterman algorithm |

`score` |
a numeric vector of island scores |

`start` |
a numeric vector of indices identifying the start of each island |

`length` |
a numeric vector of island lengths |

T.S.Price

Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol. 1981;147(1):195-7.

Price TS, et al. SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data. Nucl Acids Res. 2005;33(11):3455-3464.

`sw.threshold`

`sw.perm.test`

`sw.rob`

`sw.plot`

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