plotCorrectedCN {CRImage} | R Documentation

## 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.

### 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.

### Value

No value is returned.

### Author(s)

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

### 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)

[Package CRImage version 1.40.0 Index]