Description Usage Arguments Author(s) References See Also Examples

This function plots the sign-adjusted logratios by their chromosomal location. It can superimpose the location of the highest-scoring island found by the Smith-Waterman algorithm, the results of a robustness analysis, and the expected logratios based on known copy numbers in the test DNA.

1 2 3 4 5 |

`logratio` |
a vector of logratios, not adjusted for sign or threshold |

`location` |
a vector of chromosomal locations corresponding to the log ratios |

`threshold.func` |
threshold function: see |

`sign` |
sign of logratio adjustment: see |

`highest` |
plot location of highest-scoring island if TRUE |

`expected` |
a vector of expected copy numbers, or NULL |

`rob` |
a vector of robustness scores, or NULL |

`legend` |
plot legend if TRUE |

`xlab` |
X axis label |

`ylab` |
Y axis label |

`...` |
other arguments passed to the 'plot' function |

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.

`sw`

`sw.threshold`

`sw.perm.test`

`sw.rob`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ```
## 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 permuation test for islands identified
p <- sw.perm.test(x, max.nIslands = NULL, nIter = 1e4)
## calculate robustness scores
r <- sw.rob(x)
## plot results
sw.plot(logratio, seq(length(logratio)),
function(x) median(x) + .2 * mad(x), sign = -1, rob = r,
main = paste("Toy dataset, highest-scoring island p =", p[1]))
``` |

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cgh documentation built on May 2, 2019, 5:51 a.m.

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