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

Function to adjust intensity logratios for sign and threshold before performing the Smith-Waterman Algorithm.

1 2 3 | ```
sw.threshold(logratio,
threshold.func = function(x) median(x) + .2 * mad(x), sign = +1)
``` |

`logratio` |
a vector of real values, corresponding to fluorescence intensity logratios |

`threshold.func` |
function for calculating threshold |

`sign` |
sign of logratio adjustment |

The purpose of this function is to adjust the microarray fluorescence intensity logratios to ensure that they have the appropriate sign and a mean that is less than zero. sign = +1 is used to detect polysomy (regions of copy number change increase) in test:control logratios. Conversely, sign = -1 is used – inverting the sign of the logratios – to detect deletions (regions of copy number decrease). A threshold, calculated using the threshold function, is subtracted from the sign-adjusted logratios to ensure that they have a negative mean. The default threshold function is equal to the median, plus a small contant multiplied by a robust estimator of the standard deviation.

A numeric vector equal to

sign * logratio - threshold.func( sign * logratio )

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.

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