QuantumClone: Clustering Mutations using High Throughput Sequencing (HTS) Data
Version 1.0.0.4

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 publication2017-03-08 16:37:18
MaintainerPaul Deveau <paul.deveau@curie.fr>
LicenseGPL-2
Version1.0.0.4
URL https://github.com/DeveauP/QuantumClone
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("QuantumClone")

Getting started

Release"
Use case"

Popular man pages

add_leaf_list: Phylogenetic tree leaf
check_leaf: Check created leaf
e.step: Expectation step calculation
evolution_plot: Evolution plot
MajorityVote: Majority vote
m.step: Maximization step
One_D_plot: Plots
See all...

All man pages Function index File listing

Man pages

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

Functions

BIC_criterion Man page Source code
BIC_criterion_FLASH Man page Source code
Cellular_preclustering Man page Source code
CellularitiesFromFreq Man page Source code
Cluster_plot_from_cell Man page Source code
Compute.adj.fact Source code
Compute_NMI Man page Source code
Compute_objective Man page Source code
Create_prior_cutTree Man page Source code
EM.algo Man page Source code
EM_clustering Man page Source code
FLASH_main Man page Source code
FlashQC Man page Source code
From_freq_to_cell Man page Source code
FullEM Man page Source code
Input_Example Man page
MajorityVote Man page Source code
NMI_cutree Man page Source code
One_D_plot Man page Source code
One_step_clustering Man page Source code
Patient_schrodinger_cellularities Man page Source code
Precision_Recall Man page Source code
ProbDistMatrix Man page Source code
Probability.to.belong.to.clone Man page Source code
QC_output Man page
QuantumCat Man page Source code
QuantumClone Man page Source code
Tidy_output Man page Source code
Tree Man page
Tree_generation Man page Source code
add.to.list Source code
add_leaf_list Man page Source code
check_leaf Man page Source code
check_split Man page Source code
create_priors Man page Source code
e.step Man page Source code
eval.fik Source code
eval.fik.m Man page Source code
evolution_plot Man page Source code
filter_on_fik Man page Source code
find_x_position Man page Source code
grbase Man page
grzero Man page Source code
hard.clustering Man page Source code
is_included Man page Source code
list_prod Man page Source code
longueur Man page Source code
m.step Man page Source code
manual_plot_trees Man page Source code
multiplot_trees Man page Source code
parallelEM Man page Source code
phylo_tree_generation Man page Source code
plot_QC_out Man page Source code
plot_cell_from_Return_out Man page Source code
plot_with_margins_densities Man page Source code
strcount Man page Source code
update_probs Man page Source code
zscore Man page Source code

Files

inst
inst/doc
inst/doc/Use_case.Rmd
inst/doc/Release.html
inst/doc/Use_case.R
inst/doc/Release.Rmd
inst/doc/Use_case.html
tests
tests/reproducible_testing
tests/reproducible_testing/Rscript
tests/reproducible_testing/Rscript/filtering_pipeline_PoC.Rmd
tests/reproducible_testing/Rscript/figure3.Rmd
tests/reproducible_testing/Rscript/html_outputs.zip
tests/reproducible_testing/Rscript/optim_vs_optimx.R
tests/reproducible_testing/Rscript/reproduce.R
tests/reproducible_testing/Rscript/filtering_pipeline_PoC_2.Rmd
tests/reproducible_testing/Rscript/reproduce_2.R
tests/reproducible_testing/Rscript/parallelization.Rmd
tests/reproducible_testing/Rscript/filtering_pipeline_comp_time.Rmd
tests/reproducible_testing/Comparison_other_methods
tests/reproducible_testing/Comparison_other_methods/Pipeline_test.zip
tests/reproducible_testing/Comparison_other_methods/Plots.zip
tests/testthat.R
tests/testthat
tests/testthat/test-One_step_clustering.R
tests/testthat/test-FlashQC.R
tests/testthat/test-ProbBelClone.R
tests/testthat/test-gradienttools.R
tests/testthat/test-validations_tools.R
tests/testthat/test-plots.R
tests/testthat/test-QuantumCat.R
NAMESPACE
data
data/Tree.rda
data/Input_Example.rda
data/QC_out.rda
R
R/Cluster_selection.R
R/FlashQC.R
R/validation_tools.R
R/Phylogeny_tree.R
R/descent.R
R/EM.R
R/QuantumCat.R
R/QuantumClone.R
R/data.R
R/Tree_generation.R
R/plots.R
vignettes
vignettes/Use_case.Rmd
vignettes/Release.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/find_x_position.Rd
man/grbase.Rd
man/manual_plot_trees.Rd
man/is_included.Rd
man/FlashQC.Rd
man/update_probs.Rd
man/plot_cell_from_Return_out.Rd
man/Probability.to.belong.to.clone.Rd
man/MajorityVote.Rd
man/CellularitiesFromFreq.Rd
man/parallelEM.Rd
man/Precision_Recall.Rd
man/BIC_criterion.Rd
man/QC_output.Rd
man/Tree.Rd
man/zscore.Rd
man/check_leaf.Rd
man/EM_clustering.Rd
man/m.step.Rd
man/Tidy_output.Rd
man/One_step_clustering.Rd
man/ProbDistMatrix.Rd
man/One_D_plot.Rd
man/grzero.Rd
man/Compute_NMI.Rd
man/list_prod.Rd
man/add_leaf_list.Rd
man/Tree_generation.Rd
man/BIC_criterion_FLASH.Rd
man/e.step.Rd
man/phylo_tree_generation.Rd
man/longueur.Rd
man/Input_Example.Rd
man/Patient_schrodinger_cellularities.Rd
man/strcount.Rd
man/multiplot_trees.Rd
man/evolution_plot.Rd
man/eval.fik.m.Rd
man/plot_QC_out.Rd
man/FullEM.Rd
man/check_split.Rd
man/plot_with_margins_densities.Rd
man/filter_on_fik.Rd
man/EM.algo.Rd
man/QuantumCat.Rd
man/create_priors.Rd
man/QuantumClone.Rd
man/Cellular_preclustering.Rd
man/From_freq_to_cell.Rd
man/Compute_objective.Rd
man/NMI_cutree.Rd
man/hard.clustering.Rd
man/FLASH_main.Rd
man/Cluster_plot_from_cell.Rd
man/Create_prior_cutTree.Rd
QuantumClone documentation built on May 19, 2017, 6:28 p.m.

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