plotProfile: Static Genomic Profile Visualization

In fredcommo/rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

Description

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

Usage

## S4 method for signature 'rCGH'
plotProfile(object, showCopy=FALSE, 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"
showCopy	: logical. To show the estimated copy numbers instead of the Log2Ratios. default is FALSE.
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.

Author(s)

Frederic Commo

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 <- segmentCGH(cgh, nCores=1)
cgh <- EMnormalize(cgh)

# Static visalization using Log2Ratios
plotProfile(cgh, symbol = "erbb2")

# Static visalization using estimated copy numbers
plotProfile(cgh, showCopy = TRUE, symbol = "erbb2")

fredcommo/rCGH documentation built on May 16, 2019, 2:41 p.m.