plotProfile {rCGH} | R Documentation

## Static Genomic Profile Visualization

### 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")

[Package rCGH version 1.20.0 Index]