Clustering Mutations using High Throughput Sequencing (HTS) Data


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Documentation for package ‘QuantumClone’ version 0.15.11

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add_leaf_list Phylogenetic tree leaf
BIC_criterion Bayesian Information Criterion
CellularitiesFromFreq Cellularities from allele frequency
Cluster_plot_from_cell Cellularity clustering
create_priors Clonal fraction prior creation
e.step Expectation step calculation
EM.algo Expectation Maximization algorithm
EM_clustering Expectation Maximization
evolution_plot Evolution plot
filter_on_fik Data filter
find_x_position Graphic position
From_freq_to_cell Wrap-up function
FullEM Expectation Maximization algorithm
hard.clustering Hard clustering based on EM output
Input_Example Example generated by QuantumCat
is_included Group theory
list_prod List product
longueur Length
m.step Maximization step
manual_plot_trees Plot tree
multiplot_trees Plots multiple trees
Multitest Multiple testing
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
Probability.to.belong.to.clone Probability
QC_output Example of output generated by clustering of Input_Example
QuantumCat Data generation
QuantumClone One step analysis function
statistics_on_Multitest Multiple testing
strcount String count
ThreeD_plot 3D Plot
Tree Example of output by Tree_generation
Tree_generation Phylogenetic tree