CRImage (version 1.20.0)

plotCorrectedCN: Plot CN profiles corrected for cellularity

Description

This function takes the result of a call to correctCopyNumber and plots the results.

Usage

plotCorrectedCN(CN, chr=NULL)

Arguments

CN

object result of a call to correctCopyNumber.

chr

chromosome to plot.

Value

No value is returned.

Details

A panel with four plots is created. The top panel shows LRR (with DNAcopy segmentation overlayed) and BAF before correction and the bottom panel shows the plots after correction.

References

Yuan, Y et al. Quantitative image analysis of cellular heterogeneity in primary breast tumors enriches genomic assays. In prep.

Examples

LRR <- c(rnorm(100, 0, 1), rnorm(10, -2, 1), rnorm(20, 3, 1),
       rnorm(100,0, 1)) 
BAF <- c(rnorm(100, 0.5, 0.1), rnorm(5, 0.2, 0.01), rnorm(5, 0.8, 0.01), rnorm(10, 0.25, 0.1), rnorm(10, 0.75, 0.1),
       rnorm(100,0.5, 0.1)) 

Pos <- sample(x=1:500, size=230, replace=TRUE)
Pos <- cumsum(Pos)
Chrom <- rep(1, length(LRR))
z <- data.frame(Name=1:length(LRR), Chrom=Chrom, Pos=Pos, LRR=LRR, BAF=BAF)
res <- correctCopyNumber(arr="Sample1", chr=1, p=0.75, z=z)
plotCorrectedCN(res, chr=1)