coriell {bcp} | R Documentation |
These are two data array CGH studies of Corriel cell lines taken from the reference below.
data(coriell)
A data frame containing five variables: first is clone name, second is clone chromosome, third is clone position, fourth and fifth are log2ratio for two cell lines.
htp://www.nature.com/ng/journal/v29/n3/suppinfo/ng754_S1.html
Snijders et al. (2001), Assembly of microarrays for genome-wide measurement of DNA copy number, Nature Genetics, 29, 263-264.
##### Coriell chromosome 11 ##### data(coriell) chrom11 <- na.omit(coriell$Coriell.05296[coriell$Chromosome==11]) n <- length(chrom11) bcp.11 <- bcp(chrom11[1:n]) summary.bcp(bcp.11) plot.bcp(bcp.11) ##### Coriell chromosome 11 ##### data(coriell) chrom11 <- as.vector(na.omit(coriell$Coriell.05296[coriell$Chromosome==11])) bcp.11 <- bcp(chrom11) summary.bcp(bcp.11) plot.bcp(bcp.11) # to see bcp and Circular Binary Segmentation results run: if(require("DNAcopy")) { bcp.11$posterior.prob[length(bcp.11$posterior.brob)] <- 0 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") plot(1:n, bcp.11$posterior.mean, type="l", xlab="Location", ylab="Posterior Mean", main="Posterior Means") lines(cbs.ests, col="red") points(chrom11) plot(1:n, bcp.11$posterior.prob, type="l", ylim=c(0,1), xlab="Location", ylab="Posterior Probability of a Change", main="Change Point Locations") for(i in 1:(dim(cbs$output)[1]-1)) abline(v=cbs$output$loc.end[i], col="red") par(op) } else { cat("DNAcopy is not loaded") }