view {rCGH} | R Documentation |
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
.
## S4 method for signature 'rCGH' view(object, browser = TRUE, ...)
object |
: An object of class |
browser |
: logical. When |
... |
: Optional parameters used by |
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.
None.
Frederic Commo
plotProfile
, plotLOH
, multiplot
,
runApp
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) ## Not run: # Interactive visalizations view(cgh) ## End(Not run)