plotRatio: Plot log2Ratio intensities

In gada: Genome Alteration Detection Algorithm (GADA)

Description

This function produces a plot of log2ratios and segments by chromosome

Usage

plotRatio(x, ...)

## S3 method for class 'setupGADA'
plotRatio(x, chr, chromStart, chromEnd, B.allele.freq=FALSE, ...)

## S3 method for class 'BackwardElimination'
plotRatio(x, chr, num.points, postscript=FALSE, ...)

## S3 method for class 'parGADA'
plotRatio(x, Sample, segments=FALSE, ...)

Arguments

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

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

setupGADAIllumina, setupGADAaffy, SBL, BackwardElimination

Examples

## 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)

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