plotWG: Plot Whole Genome

In gada: Genome Alteration Detection Algorithm (GADA)

Description

Plots altered probes, in a given proportion of individuals, for the entire genome when several samples are analyzed

Usage

plotWG(x, min.percentage=0.05, max.number.cnv=100, length.base, chr=c(1:22,"X","Y"))

Arguments

x	An object of class 'summaryparGADA'
min.percentage	The minimum percentage of individuals with a shared altered segment to be plotted. The default is 0.05 (e.g., 5%)
max.number.cnv	For a given chromosome, the maximum number of altered segments found in a given individual. The default is 100. If the number of segments for a given individual is larger than 'max.number.cnv' this sample is discarded.
length.base	a vector with two components. The first corresponds to the minimum size required to consider a segment as a CNV, while the second one corresponds to the maximum size. If missing, this information is obtained from the attribute 'length.base' of object 'x'.
chr	A vector indicating the chromosomes to be plotted. The default is c(1:22, "X", "Y")

Value

No return value, just the plot

References

Pique-Regi R, Caceres A, Gonzalez JR. "R-Gada: a package for fast detection and visualization of copy number alterations on multiple samples", BMC Bioinformatics , Submitted Nov 2009

See Also

parBE, parSBL

Examples

## Not run: 
###
### First step (required)
### 

# Read data 
# a folder called rawData containing a file for each individual is required

# Illumina data
myExample<-setupParGADAIllumina(log2ratioCol=4, NumCols=5)

# Affymetrix data
myExample<-setupParGADAaffy(log2ratioCol=4, NumCols=5)

###
### Second step
### 

# segmentation for all samples
parSBL(myExample, estim.sigma2=TRUE, aAlpha=0.8)
parBE(myExample,T=8, MinSegLen=8)

###
### Third step
### 

# summaryze all samples
allSamples<-summary(myExample)

# plot entire genome
plotWG(allSamples)

# plot a given chromosome
plot(allSamples, chr=6)


## End(Not run)

gada documentation built on May 2, 2019, 6:10 p.m.