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##### Coriell chromosome 11 #####
data(coriell)
chrom11 <- as.vector(na.omit(coriell$Coriell.05296[coriell$Chromosome==11]))
bcp.11 <- bcp(chrom11)
plot(bcp.11, main="Coriell chromosome 11 (bcp)")
# To see bcp and Circular Binary Segmentation results, using
# base graphics (see plot.bcp.legacy for more examples):
if(require("DNAcopy")) {
n <- length(chrom11)
cbs <- segment(CNA(chrom11, rep(1, n), 1:n), verbose = 0)
cbs.ests <- rep(unlist(cbs$output[6]), unlist(cbs$output[5]))
op <- par(mfrow=c(2,1),col.lab="black",col.main="black")
op2 <- par(mar=c(0,4,4,2),xaxt="n", cex.axis=0.75)
plot(1:n, bcp.11$data[,2], col="grey", pch=20, xlab="Location",
ylab="Posterior Mean",
main="Coriell chromosome 11 (DNAcopy)")
lines(cbs.ests, col="red")
lines(bcp.11$posterior.mean, lwd=2)
par(op2)
op3 <- par(mar=c(5,4,0,2), xaxt="s", cex.axis=0.75)
plot(1:n, bcp.11$posterior.prob, type="l", ylim=c(0,1),
xlab="Location", ylab="Posterior Probability", main="")
for (i in 1:(dim(cbs$output)[1]-1)) {
abline(v=cbs$output$loc.end[i], col="red")
}
par(op3)
par(op)
} else {
cat("DNAcopy is not loaded")
}
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