Clustering Mutations using High Throughput Sequencing (HTS) Data


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Documentation for package ‘QuantumClone’ version 1.0.0.6

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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_priors Clonal fraction prior creation
Create_prior_cutTree Create priors from hierarchical clustering
e.step Expectation step calculation
EM.algo Expectation Maximization algorithm
EM_clustering Expectation Maximization
eval.fik.m Eval probability for M step Computes the log directly as log density is faster to compute
evolution_plot Evolution plot
filter_on_fik Data filter
find_x_position Graphic position
FlashQC Flash QuantumClone
FLASH_main Flash core
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
m.step Maximization step
MajorityVote Majority vote
manual_plot_trees Plot tree
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