QuantumClone: Clustering Mutations using High Throughput Sequencing (HTS) Data

Using HTS data, clusters mutations in order to recreate putative clones from the data provided. It requires genotype at the location of the variant as well as the depth of coverage and number of reads supporting the mutation. Additional information may be provided, such as the contamination in the tumor sample. This package also provides a function QuantumCat() which simulates data obtained from tumor sequencing.

Author
Paul Deveau [aut, cre]
Date of publication
2016-08-26 14:28:21
Maintainer
Paul Deveau <paul.deveau@curie.fr>
License
GPL-2
Version
0.16.8.19
URLs

View on CRAN

Man pages

add_leaf_list
Phylogenetic tree leaf
BIC_criterion
Bayesian Information Criterion
CellularitiesFromFreq
Cellularities from allele frequency
Cluster_plot_from_cell
Cellularity clustering
Compute_NMI
Normalized Mutual Information
create_priors
Clonal fraction prior creation
EM.algo
Expectation Maximization algorithm
EM_clustering
Expectation Maximization
e.step
Expectation step calculation
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
manual_plot_trees
Plot tree
m.step
Maximization step
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
Tidy_output
Tidying output from EM
Tree
Example of output by Tree_generation
Tree_generation
Phylogenetic tree

Files in this package

QuantumClone
QuantumClone/inst
QuantumClone/inst/doc
QuantumClone/inst/doc/Use_case.Rmd
QuantumClone/inst/doc/Release.html
QuantumClone/inst/doc/Use_case.R
QuantumClone/inst/doc/Release.Rmd
QuantumClone/inst/doc/Use_case.html
QuantumClone/NAMESPACE
QuantumClone/data
QuantumClone/data/Tree.rda
QuantumClone/data/Input_Example.rda
QuantumClone/data/QC_out.rda
QuantumClone/R
QuantumClone/R/Phylogeny_tree.R
QuantumClone/R/EM.R
QuantumClone/R/QuantumCat.R
QuantumClone/R/QuantumClone.R
QuantumClone/R/data.R
QuantumClone/R/plots.R
QuantumClone/vignettes
QuantumClone/vignettes/Use_case.Rmd
QuantumClone/vignettes/Release.Rmd
QuantumClone/MD5
QuantumClone/build
QuantumClone/build/vignette.rds
QuantumClone/DESCRIPTION
QuantumClone/man
QuantumClone/man/find_x_position.Rd
QuantumClone/man/Multitest.Rd
QuantumClone/man/manual_plot_trees.Rd
QuantumClone/man/is_included.Rd
QuantumClone/man/plot_cell_from_Return_out.Rd
QuantumClone/man/Probability.to.belong.to.clone.Rd
QuantumClone/man/CellularitiesFromFreq.Rd
QuantumClone/man/parallelEM.Rd
QuantumClone/man/BIC_criterion.Rd
QuantumClone/man/QC_output.Rd
QuantumClone/man/Tree.Rd
QuantumClone/man/EM_clustering.Rd
QuantumClone/man/m.step.Rd
QuantumClone/man/Tidy_output.Rd
QuantumClone/man/One_step_clustering.Rd
QuantumClone/man/One_D_plot.Rd
QuantumClone/man/Compute_NMI.Rd
QuantumClone/man/list_prod.Rd
QuantumClone/man/add_leaf_list.Rd
QuantumClone/man/Tree_generation.Rd
QuantumClone/man/e.step.Rd
QuantumClone/man/phylo_tree_generation.Rd
QuantumClone/man/longueur.Rd
QuantumClone/man/Input_Example.Rd
QuantumClone/man/Patient_schrodinger_cellularities.Rd
QuantumClone/man/strcount.Rd
QuantumClone/man/multiplot_trees.Rd
QuantumClone/man/evolution_plot.Rd
QuantumClone/man/plot_QC_out.Rd
QuantumClone/man/FullEM.Rd
QuantumClone/man/statistics_on_Multitest.Rd
QuantumClone/man/plot_with_margins_densities.Rd
QuantumClone/man/filter_on_fik.Rd
QuantumClone/man/EM.algo.Rd
QuantumClone/man/QuantumCat.Rd
QuantumClone/man/create_priors.Rd
QuantumClone/man/QuantumClone.Rd
QuantumClone/man/From_freq_to_cell.Rd
QuantumClone/man/hard.clustering.Rd
QuantumClone/man/Cluster_plot_from_cell.Rd