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??)