CloneTracer output

CloneTracer outputs <br> tar.gz file which contains for each patient a list with the following items: <br> patient: patient name M: matrix with mutant counts (mutationsxcells) N: matrix with reference counts (mutationsxcells) mutations_matrix: column names of M and N matrix with mutation names cell_barcode: rownames of M and N matrix trees: clonal hierarchies with the highest evidence according to CloneTracer. Binary encoding (0: abscence of mutation ; 1: presence of mutation) mutations_tree: column names of trees tree_indices: indices of selected trees over all potential_trees (only required for internal functions) clonal_prob: list of matrices with clonal probabilities corresponding to trees listed in trees slot selected_tree: tree selected for downstream analysis selected_clonal_probs: clonal probabilities of selected tree selected_tree_ind: index of selected tree ELBO: ELBO values for all trees stored in potential_trees slot. potential_trees: list of trees evaluated in the last inference step of the model. children and parent: only required for internal functions. <br> We provide costumised functions and example vignettes to visualize this type of data in https://github.com/veltenlab/CloneTracer/tree/master/clonal_inference/vignettes