Description Usage Arguments Value References See Also Examples
Plots altered probes, in a given proportion of individuals, for the entire genome when several samples are analyzed
1 |
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") |
No return value, just the plot
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | ## 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)
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