Description Usage Arguments Value References See Also Examples
This function produces a plot of log2ratios and segments by chromosome
1 2 3 4 5 6 7 8 9 10 |
x |
An object of class 'setupGADA', 'BackwardElimination', or 'parGADA' |
chr |
A given cromosome |
chromStart |
The beginning of the cromosome |
chromEnd |
The end of the cromosome |
B.allele.freq |
The function is prepared to show B-allele frequency for Illumina data in future versions. This should not be changed. The defaul is FALSE |
num.points |
The desired number of log2ratio intensities to be showed in the plot. This is useful for importing figures |
postscript |
Is the plot exported to a encapsulated postscript file? the default is FALSE |
Sample |
The sample to be plotted. This is required when an object of class 'parGADA' is passed through the argument 'x' |
segments |
Are segments added to the plot? This can be used when an object of class 'parGADA' is passed through the argument 'x' |
... |
Other arguments passes through the function plotlogRatio |
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
setupGADAIllumina
, setupGADAaffy
, SBL
, BackwardElimination
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 | ## Not run:
## Simulated data
set.seed(123456)
cn<-rep(c(rep(1,1E5-100),rep(1,100),rep(1,1E5)),4) #Underlying copy number
arrayData<-rnorm(length(cn),mean=(log2(cn)-1),sd=1) #Simulated array
dataSim<-setupGADAgeneral(arrayData)
plotRatio(dataSim)
## Real data
# import data
download.file("http://www.creal.cat/jrgonzalez/GADA/dataIllumina.txt","dataIllumina.txt")
# creating object of class setupGADA
dataIllumina<-setupGADAIllumina(file="dataIllumina.txt", log2ratioCol=5, NumCols=6)
# Segmentation procedure
step1<-SBL(dataIllumina, estim.sigma2=TRUE)
step2<-BackwardElimination(step1,T=4.5,MinSegLen=3)
# plot log2ratio intensities
plotRatio(dataIllumina)
# plot log2ratio intensities for chromosome 12
plotRatio(dataIllumina, chr=12)
# plot log2ratio intensities and segments
plotRatio(step2)
## End(Not run)
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