Optimization of clone positions and proportion of mutations in each clone, based on the previously calculated expectation
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fik |
Matrix giving the probability of each mutation to belong to a specific clone |
Schrod |
A list of dataframes (one for each sample), generated by the Patient_schrodinger_cellularities() function. |
previous.weights |
Weights from the previous optimization step (used as priors for this step) |
previous.centers |
Clone coordinates from previous optimization step (used as priors for this step) |
contamination |
Numeric vector with the fraction of normal cells contaminating the sample |
adj.factor |
Factor to compute the probability: makes transition between the cellularity of the clone and the frequency observed |
optim |
use L-BFS-G optimization from R ("default"), or from optimx ("optimx"), or Differential Evolution ("DEoptim") |
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