cgh (version 1.0-7.1)

sw.threshold: Threshold function

Description

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

Usage

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

Arguments

logratio

a vector of real values, corresponding to fluorescence intensity logratios

threshold.func

function for calculating threshold

sign

sign of logratio adjustment

Value

A numeric vector equal tosign * logratio - threshold.func( sign * logratio )

Details

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.

References

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.

See Also

sw

Examples

## 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)