plotCorrectedCN: Plot CN profiles corrected for cellularity
In CRImage: CRImage a package to classify cells and calculate tumour cellularity

Description Usage Arguments Details Value Author(s) References Examples

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

1	plotCorrectedCN(CN, chr=NULL)

`CN`	object result of a call to `correctCopyNumber`.
`chr`	chromosome to plot.

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.

No value is returned.

Oscar M. Rueda, rueda.om@gmail.com

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

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)