Hello I just started using sciClone and I wanted to get familiar with it using the example data and script listed on the github and I just have two quick questions:
In the example plots, three different cases were analyzed based on the number of input vafs from three related tumor samples. So, for example, for 1d outputs there are three files, one for each call of the sciClone() function. My question is, should the results be identical if you just called the function once, say for example for three different tumor samples? In the file 'clusters3.1d.pdf' there are three pages, one clonality plot for each sample. If you compare the first page of that file to the first page of the file 'clusters1.1d.pdf' - the results are indeed identical. But if you compare the second page of the file 'clusters3.1d.pdf' to the second page of the file 'clusters2.1d.pdf', it is not identical (as in there are 5 clusters in the 'clusters2.1d.pdf' as opposed to the two clusters in the 'clusters4.1d.pdf' files). Also if you compare the 2d cluster results, again the scenario where 2 tumor vafs were provided as inputs there are 5 clusters, but in the scenario with 3 tumor vafs on the 'Sample1 vs Sample2' graph, there are two clusters. Is this some important difference, or why is this being expressed like this?
If I have more than three vaf tumor inputs, what will the outputs be like? Will the 3d output file give multiple graphs, one for each combination of three samples, eg 1-2-3, 1-3-4 and 2-3-4, or is the maximum number of vaf inputs 3?
Thank you for any answers in advance and sorry if something like this has already been asked. With respect, Uros Sipetic