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.

AuthorPaul Deveau [aut, cre]
Date of publication2016-08-26 14:28:21
MaintainerPaul Deveau <paul.deveau@curie.fr>
LicenseGPL-2
Version0.16.8.19
https://github.com/DeveauP/QuantumClone

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

Functions

add_leaf_list Man page
BIC_criterion Man page
CellularitiesFromFreq Man page
Cluster_plot_from_cell Man page
Compute_NMI Man page
create_priors Man page
EM.algo Man page
EM_clustering Man page
e.step Man page
evolution_plot Man page
filter_on_fik Man page
find_x_position Man page
From_freq_to_cell Man page
FullEM Man page
hard.clustering Man page
Input_Example Man page
is_included Man page
list_prod Man page
longueur Man page
manual_plot_trees Man page
m.step Man page
multiplot_trees Man page
Multitest Man page
One_D_plot Man page
One_step_clustering Man page
parallelEM Man page
Patient_schrodinger_cellularities Man page
phylo_tree_generation Man page
plot_cell_from_Return_out Man page
plot_QC_out Man page
plot_with_margins_densities Man page
Probability.to.belong.to.clone Man page
QC_output Man page
QuantumCat Man page
QuantumClone Man page
statistics_on_Multitest Man page
strcount Man page
Tidy_output Man page
Tree Man page
Tree_generation Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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