plotProfile {rCGH} | R Documentation |
This function display a static view of the genomic profile stored in an
object of class "rCGH"
.
## 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)
object |
: An object of class |
showCopy |
: logical. To show the estimated copy numbers instead of the Log2Ratios.
default is |
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 |
pCol |
: string. The probe points color. DEfault is |
GLcol |
: vector. A vector of 2 colors: the gained and lost segments colors,
respectively. Default is |
Title |
: character string. A title for the density plot. If |
ylim |
: numeric. A vector of two values specifying a range for the y-axis.
If |
None.
Frederic Commo
plotDensity
, plotLOH
, multiplot
,
view
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")