Man pages for QuantumClone
Clustering Mutations using High Throughput Sequencing (HTS) Data

add_leaf_listPhylogenetic tree leaf
BIC_criterionBayesian Information Criterion
BIC_criterion_FLASHCompute criterion FLASH
CellularitiesFromFreqCellularities from allele frequency
Cellular_preclusteringPreclustering method
check_leafCheck created leaf
check_splitCheck
Cluster_plot_from_cellCellularity clustering
Compute_NMINormalized Mutual Information
Compute_objectiveCompute value of objective function
Create_prior_cutTreeCreate priors from hierarchical clustering
create_priorsClonal fraction prior creation
EM.algoExpectation Maximization algorithm
EM_clusteringExpectation Maximization
e.stepExpectation step calculation
eval.fik.mEval probability for M step Computes the log directly as log...
evolution_plotEvolution plot
filter_on_fikData filter
find_x_positionGraphic position
FLASH_mainFlash core
FlashQCFlash QuantumClone
From_freq_to_cellWrap-up function
FullEMExpectation Maximization algorithm
grbaseComputes gradient of function
grzeroGradient 0
hard.clusteringHard clustering based on EM output
Input_ExampleExample generated by QuantumCat
is_includedGroup theory
list_prodList product
longueurLength
MajorityVoteMajority vote
manual_plot_treesPlot tree
m.stepMaximization step
multiplot_treesPlots multiple trees
NMI_cutreeNMI
One_D_plotPlots
One_step_clusteringCellularity clustering
parallelEMExpectation Maximization algorithm
Patient_schrodinger_cellularitiesPatient Schrodinger Cellularities
phylo_tree_generationData generation
plot_cell_from_Return_outPlot cellularity
plot_QC_outPlot QC_output
plot_with_margins_densitiesPlot with margin densities
Precision_RecallPrecision
Probability.to.belong.to.cloneProbability
ProbDistMatrixDistance
QC_outputExample of output generated by clustering of Input_Example
QuantumCatData generation
QuantumCloneOne step analysis function
strcountString count
Tidy_outputTidying output from EM
TreeExample of output by Tree_generation
Tree_generationPhylogenetic tree
update_probsUpdate proportions
zscoreZ-score
QuantumClone documentation built on Nov. 17, 2017, 5:24 a.m.