rCGH (version 1.2.2)

view: Interactive Genomic Profile Visualization

Description

This function is build on top of shiny, and provides an iteractive way for visualizing a genomic profile, and exploring the list of genes. From a command panel, the user can interact with the graph in different ways. See details.

Usage

## S3 method for class 'rCGH':
view(object, browser = TRUE, ...)

Arguments

object

: An object of class "rCGH"

browser

: logical. When TRUE (default), the system's default web browser will be launched automatically.

...

: Optional parameters used by runApp.

Value

• None.

Details

The left command panel allows the user several actions:

• displaying a specific gene by calling its HUGO symbol.
• showing all or one unique chromosome.
• merging segments shorter than a specified value, in Kb.
• recentering the entire profile.
• rescaling the y-axis.
• specifying the Log2Ratio cut offs for defining gains and losses.
• specifying a segment lenght cut off, in Mb.
• exporting the genomic plot.
• exporting the genes list.

Some actions, such as showing one unique chromosome or specifying cut offs (gain, loss, segment length), automatically update the gene table available in the "Genes table" tab.

See Also

plotProfile, plotLOH, multiplot, runApp

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)

# Interactive visalizations
view(cgh)