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.
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sw.threshold(logratio, threshold.func = function(x) median(x) + .2 * mad(x), sign = +1)
a vector of real values, corresponding to fluorescence intensity logratios
function for calculating threshold
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 )
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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