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
Olshen, A. B., Venkatraman, E. S., Lucito, R., Wigler, M. (2004), Circular binary segmentation for the analysis of array-based DNA copy number data, Biostatistics, 5, 557-572. url: http://www.bioconductor.org/repository/release1.5/package/html/DNAcopy.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]) plot.bcp(bcp.11) ##### Coriell chromosome 11 ##### data(coriell) chrom11 <- as.vector(na.omit(coriell$Coriell.05296[coriell$Chromosome==11])) bcp.11 <- bcp(chrom11) plot.bcp(bcp.11) # to see bcp and Circular Binary Segmentation results run: 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$data, col="grey", pch=20, xlab="Location", ylab="Posterior Mean", main="Posterior Means and Probabilities of a Change") lines(cbs.ests, col="red") lines(bcp.11$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") }