sw.threshold: Threshold function
In cgh: Microarray CGH analysis using the Smith-Waterman algorithm

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

View source: R/cgh.R

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)

`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.

sw

## 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), sign = -1)

## perform Smith-Waterman algorithm
sw(x, trace = TRUE)