Clustering cellularities based on the most likely presence of a clone, using the pamk algorithm (fpc package). Clustering can be guided by toggling manual_clustering on and/or giving a range of number of clusters.
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Cell |
Output from Return_one_cell_by_mut, list of cellularities (one list-element per sample) |
Sample_names |
Name of the sample |
simulated |
Was the data generated by QuantumCat? |
save_plot |
Should the clustering plots be saved? Default is True |
contamination |
The fraction of normal cells in the samples |
clone_priors |
If known a list of priors (cell prevalence) to be used in the clustering |
prior_weight |
If known a list of priors (fraction of mutations in a clone) to be used in the clustering |
nclone_range |
Number of clusters to look for |
Initializations |
Maximal number of independant initial condition tests to be tried |
preclustering |
The type of preclustering used for priors: "Flash","kmedoid" or NULL. NULL will generate centers using uniform distribution. |
epsilon |
Stop value: maximal admitted value of the difference in cluster position and weights between two optimization steps. |
ncores |
Number of CPUs to be used |
output_directory |
Directory in which to save results |
model.selection |
The function to minimize for the model selection: can be "AIC", "BIC", or numeric. In numeric, the function uses a variant of the BIC by multiplication of the k*ln(n) factor. If >1, it will select models with lower complexity. |
optim |
use L-BFS-G optimization from R ("default"), or from optimx ("optimx"), or Differential Evolution ("DEoptim") |
keep.all.models |
Should the function output the best model (default; FALSE), or all models tested (if set to true) |
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