adjustSignal {rCGH} | R Documentation |
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.
## 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 |
Scale |
: logical. If |
Cy |
: logical. If |
GC |
: logical. If |
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 |
nCores |
: numeric. The number of cores to use in order to speed up the computation.
When |
verbose |
: logical. When |
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
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)