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

Perform a permutation test of island scores from the Smith-Waterman algorithm.

1 2 | ```
sw.perm.test(x, max.nIslands = 1, nIter = 1000, seed = NULL, trace = FALSE)
``` |

`x` |
a vector of real values |

`max.nIslands` |
number of iterations of the algorithm, each iteration finding the next highest-scoring 'island' of positive values, or NULL to find all islands |

`nIter` |
number of permutations of the input data used in the test |

`seed` |
seed for the random number generator, or NULL to use a faster random number generator that cannot be seeded |

`trace` |
print verbose output if TRUE |

A vector of probability values, calculated as the proportion of instances for which performing the Smith-Waterman algorithm on random permutations of the data identifies a higher-scoring island than the islands identified when the algorithm is performed on the original data

T.S.Price

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.

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
## simluate vector of logratios
set.seed(3)
logratio <- c(rnorm(20) - 1, rnorm(20))
## invert sign of values and subtract threshold to ensure negative mean
x <- sw.threshold(logratio, function(x) median(x) + .2 * mad(x), -1)
## perform Smith-Waterman
sw(x)
## perform permutation test on the islands identified
sw.perm.test(x, max.nIslands = NULL, nIter= 1e4)
``` |

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