add_leaf_list | Phylogenetic tree leaf |
BIC_criterion | Bayesian Information Criterion |
BIC_criterion_FLASH | Compute criterion FLASH |
CellularitiesFromFreq | Cellularities from allele frequency |
Cellular_preclustering | Preclustering method |
check_leaf | Check created leaf |
check_split | Check |
Cluster_plot_from_cell | Cellularity clustering |
Compute_NMI | Normalized Mutual Information |
Compute_objective | Compute value of objective function |
Create_prior_cutTree | Create priors from hierarchical clustering |
create_priors | Clonal fraction prior creation |
EM.algo | Expectation Maximization algorithm |
EM_clustering | Expectation Maximization |
e.step | Expectation step calculation |
eval.fik.m | Eval probability for M step Computes the log directly as log... |
evolution_plot | Evolution plot |
filter_on_fik | Data filter |
find_x_position | Graphic position |
FLASH_main | Flash core |
FlashQC | Flash QuantumClone |
From_freq_to_cell | Wrap-up function |
FullEM | Expectation Maximization algorithm |
grbase | Computes gradient of function |
grzero | Gradient 0 |
hard.clustering | Hard clustering based on EM output |
Input_Example | Example generated by QuantumCat |
is_included | Group theory |
list_prod | List product |
longueur | Length |
MajorityVote | Majority vote |
manual_plot_trees | Plot tree |
m.step | Maximization step |
multiplot_trees | Plots multiple trees |
NMI_cutree | NMI |
One_D_plot | Plots |
One_step_clustering | Cellularity clustering |
parallelEM | Expectation Maximization algorithm |
Patient_schrodinger_cellularities | Patient Schrodinger Cellularities |
phylo_tree_generation | Data generation |
plot_cell_from_Return_out | Plot cellularity |
plot_QC_out | Plot QC_output |
plot_with_margins_densities | Plot with margin densities |
Precision_Recall | Precision |
Probability.to.belong.to.clone | Probability |
ProbDistMatrix | Distance |
QC_output | Example of output generated by clustering of Input_Example |
QuantumCat | Data generation |
QuantumClone | One step analysis function |
strcount | String count |
Tidy_output | Tidying output from EM |
Tree | Example of output by Tree_generation |
Tree_generation | Phylogenetic tree |
update_probs | Update proportions |
zscore | Z-score |
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