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 1.38.0 Index]