The Progenetix CNV visualization includes some default clustering for sample CNV profiles and collation CNV frequencies.
The resource uses a standard CNV binning model with (in GRCh38) 3102 intervals of 1MB default size. For the clustering of both status and frequency values, gain and loss intervals are treated independently, resulting in 6204 values per sample (or collation) for the generation of a clustering matrix.
On the website sample and/or collation clustering is involved automatically on the
“Data Visualization” page which can be accessed from the search results. Clustering as
well as CNV visualization are performed through the PGX
Perl library, utilizing the
Algorithm::Cluster interface to the C cluster library with
m: pairwise complete-linkage clustering
e: Euclidean distance
Clustering can be omitted by setting
Cluster Tree Width to
More information is made availanble in the Use Cases category.