How can I (preferably in R/Bioconductor) perform Hierarchical clustering on CBS-segmented tumor-samples (CNV analysis)?
I have copy number variation data on 50 tumor samples. I have already preprocessed them to Log R ratios and CBS-segmented them. For each tumor sample, I have information available on variables like "tumor stage", "hasMutationInGeneX", "isPrimaryTumor", "ageOfDiagnosis" etcetera. I am interested if I can find groups of tumors (patients) that share similar copy number profiles so I want to do hierarchical clustering on the CBS-segmentation output.
Now I know their are lots of hierarcical clustering programs for microarray-expression data but I think I cannot use them. The point is that for microarray expression the output can be stored in a matrix where each row represents a shared feature by all samples:
probes Sample1 Sample2 SampleN 10101_at 0.2 0.7 -0.2 01010_at -0.3 -0.2 -1.2
However, concerning CNV-analysis the segmentation on different samples does not have features like probes that are measured in each sample, in stead you get something like this:
chr start end sample meanCopyNumber 1 100 8000 Sample1 0.2 1 200 500 Sample2 0.3
Though I am aware of packages like reshape can slice and dice data frames to get them in the desired format, I wonder if there are Biocondcutor packages that take CBS-output and do hierarchical clustering (and maybe even heatmap + dendrogram visualization??)