rCGH (version 1.2.2)

multiplot: Static Genomic Profile and LOH Visualization

Description

This function display a static view of the genomic profile and the allelic difference stored in an object of class "rCGH". If no allelic difference is available, the genomic profile only is displayed.

Usage

## S3 method for class 'rCGH':
multiplot(object, symbol=NULL, gain=.5, loss=(-.5), minLen=10,
    pCol = "grey50", GLcol = c("blue", "red3"),
    L=matrix(seq(1, 12)), p=c(2/3, 1/3), Title=NULL, ylim=NULL)

Arguments

object

: An object of class "rCGH"

symbol

: character. A valid HUGO symbol (case insensitive).

gain

: numeric. A gain threshold value (in $Log2(Ratio)$) from where gained segments will be shown, in blue.

loss

: numeric. A loss threshold value (in $Log2(Ratio)$) from where lossed segments will be shown, in red.

minLen

: numeric. The mininal length for a segment, in Kb. When NULL (default), segments are reported as they have been computed with segmentCGH, segments shorter than the specified value are re-merged otherwise.

pCol

: string. The probe points color. DEfault is "grey50".

GLcol

: vector. A vector of 2 colors: the gained and lost segments colors, respectively. Default is "blue" for gains and "red3" for losses.

L

: matrix. A matrix defining how the layout is built. Default is 12 lines.

p

: numeric. The proportion of each plot in the plot window. Default is 2/3, 1/3, which corresponds to 8 and 4 lines for the genomic profile and the LOH plot, respectiviely.

Title

: character string. A title for the density plot. If NULL (default), the sample name (when exists) will be used.

ylim

: numeric. A vector of two values specifying the y-axis range. See plotProfile.

Value

• None.

See Also

plotDensity, plotProfile, plotLOH, view

Examples

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

# Static visalizations
multiplot(cgh, "erbb2")