R CGH IV: DNAcopy

Here you will make copy number profiles for the first 10 samples, and describe their profiles.

• First extract the first 10 columns with log2.ratios and store it in a variable named dat
• Then create a CNA object with

CNAobj <- CNA(dat, colorectal$clones.info$Chrom,
              colorectal$clones.info$kb, sampleid =         )

• Next you need to create a smoothed CNA object using smooth.CNA()
• Then perform segmentation using seqment()
• Finally plot your segmented and smoothed CNA object. If you use the function pdf() before your plot, you can save all 10 plots in the same file:

pdf(file="     ")
plot(           )
dev.off()

2. Look at your plots and write which of them has a. flat profiles b. segmental gains/losses c. whole chromosome gain/loss

---

Next: GLAD

Previous: aCGH