library(cghFLasso)
data(CGH)
#############
### Example 1: Process one chromosome vector without using normal references.
CGH.FL.obj1<-cghFLasso(CGH$GBM.y)
plot(CGH.FL.obj1, index=1, type="Lines")
#############
### Example 2: Process a group of CGH arrays and use normal reference arrays.
Normal.FL<-cghFLasso.ref(CGH$NormalArray, chromosome=CGH$chromosome)
Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)
### Plot for the first arrays
i<-1
plot(Disease.FL, index=i, type="Single")
title(main=paste("Plot for the ", i ,"th BAC array", sep=""))
### Consensus plot
plot(Disease.FL, index=1:4, type="Consensus")
title(main="Consensus Plot for 4 BAC arrays")
### Plot all arrays
plot(Disease.FL, index=1:4, type="All")
title(main="Plot for all 4 arrays")
### Report and output
report<-summary(Disease.FL, index=1:4)
print(report)
output.cghFLasso(report, file="CGH.FL.output.txt")
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