rCGH (version 1.2.2)

plotProfile: Static Genomic Profile Visualization

Description

This function display a static view of the genomic profile stored in an object of class "rCGH".

Usage

## S3 method for class 'rCGH':
plotProfile(object, symbol=NULL, gain=.5, loss=(-.5),
    minLen = 10, pCol = "grey50", GLcol = c("blue", "red3"),
    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.

Title

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

ylim

: numeric. A vector of two values specifying a range for the y-axis. If NULL (default), the range of Log2Ratio is used.

Value

• None.

See Also

plotDensity, plotLOH, multiplot, 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
plotProfile(cgh, "erbb2")