Figure 1

Overall view of CGH-Plotter v2. CGH data, chromosome indices, basepairs and names of the samples are input into CGH-Plotter. Further, the type of the filter and the size of the window, which are used in filtering phase, are inputs if constant levels are calculated with dynamic programming algorithm. CGH-Plotter clusters the filtered data into three clusters with k-means clustering algorithm. Clustered data are delivered to the function, which computes the maximum number of the change points. The number of changes is needed when dynamic programming algorithm computes the gains and losses [7]. Other option is to smooth the data with basepair location based filter. Known gaps and the window size for filtering needs to be input in basepair units. Further, if interpolation wanted to take place, new basepair locations for genes with need for copy number value has to be given to CGH-Plotter. The results of the analyses can be plotted and saved into ASCII-file.