adjustSignal: Array-based CGH Preprocessing
In rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

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

This function performs several preprocessing steps: local regressions (loessFit) are used to correct cy3/cy5 and GC% bias, when Agilent dual-color hybridization are used only.
In case of Affymetrix cychp.txt (or cnchp.txt) data are used, these steps have been already done in ChAS or Affymetrix Power Tools.

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## S4 method for signature 'rCGH'
adjustSignal(object, Scale=TRUE, Cy=TRUE, GC=TRUE, Ref="cy3",
    suppOutliers=TRUE, nCores=NULL, verbose=TRUE)

`object`	: An object of class `"rCGH"`
`Scale`	: logical. If `TRUE` (default), Log2Ratios are standardized.
`Cy`	: logical. If `TRUE` (default), cy3/cy5 bias is corrected using a local regression (loessFit). For Agilent dual-color hybridization only. Notice that, in case of Affymetrix files (cychp.txt or cnchp.txt), this argument is automatically set to `FALSE`, since this step is managed when files are exported from ChAS or APT.
`GC`	: logical. If `TRUE` (default), the GC% bias is corrected using a local regression (loessFit). For Agilent dual-color hybridization only. Notice that, in case of Affymetrix files (cychp.txt or cnchp.txt), this argument is automatically set to `FALSE`, since this step is managed when files are exported from ChAS or APT.
`Ref`	: string. Which cyanine was used as the reference. Possible values are "cy3" (default) and "cy5". For Agilent dual-color hybridization only.
`suppOutliers`	: logical. If `TRUE` (default), outliers are removed using an Expectation-Maximization algorithm (EM). See `details` below.
`nCores`	: numeric. The number of cores to use in order to speed up the computation. When `NULL` (default), half of the available cores are used. If a value greater than the number of available cores is passed, this latter will be used. See `detectCores`.
`verbose`	: logical. When `TRUE` (default), progress is printed.

When suppOutliers is TRUE (default), the Log2Ratios are splitted with respect to chromosomes. The main regions within each chromosome are identified using EM. Within each region r_i, x[r_i] values are redifined according to the corresponding model parameters. as:

x[r_i] ~ N(mu_i, sigma_i)

Notice that this step may substantially increase the computation time.

An object of class "rCGH"

Frederic Commo

detectCores, mclapply

filePath <- system.file("extdata", "Affy_cytoScan.cyhd.CN5.CNCHP.txt.bz2",
    package = "rCGH")
cgh <- readAffyCytoScan(filePath, sampleName = "AffyScHD")
cgh <- adjustSignal(cgh, nCores=1)
getParam(cgh)