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.

Install the latest version of this package by entering the following in R:
install.packages("QuantumClone")
AuthorPaul Deveau [aut, cre]
Date of publication2017-03-08 16:37:18
MaintainerPaul Deveau <paul.deveau@curie.fr>
LicenseGPL-2
Version1.0.0.4
https://github.com/DeveauP/QuantumClone

View on CRAN

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

add_leaf_list Man page
BIC_criterion Man page
BIC_criterion_FLASH Man page
CellularitiesFromFreq Man page
Cellular_preclustering Man page
check_leaf Man page
check_split Man page
Cluster_plot_from_cell Man page
Compute_NMI Man page
Compute_objective Man page
Create_prior_cutTree Man page
create_priors Man page
EM.algo Man page
EM_clustering Man page
e.step Man page
eval.fik.m Man page
evolution_plot Man page
filter_on_fik Man page
find_x_position Man page
FLASH_main Man page
FlashQC Man page
From_freq_to_cell Man page
FullEM Man page
grbase Man page
grzero Man page
hard.clustering Man page
Input_Example Man page
is_included Man page
list_prod Man page
longueur Man page
MajorityVote Man page
manual_plot_trees Man page
m.step Man page
multiplot_trees Man page
NMI_cutree 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
Precision_Recall Man page
Probability.to.belong.to.clone Man page
ProbDistMatrix Man page
QC_output Man page
QuantumCat Man page
QuantumClone Man page
strcount Man page
Tidy_output Man page
Tree Man page
Tree_generation Man page
update_probs Man page
zscore Man page

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

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