CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution

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Documentation for package ‘CIMICE’ version 1.10.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

annotate_mutational_matrix	Add samples and genes names to a mutational matrix
binary_radix_sort	Radix sort for a binary matrix
build_subset_graph	Remove transitive edges and prepare graph
build_topology_subset	Compute subset relation as edge list
chunk_reader	Gradually read a file from disk
CIMICE	CIMICE Package
compact_dataset	Compact dataset rows
computeDWNW	Down weights computation
computeDWNW_aux	Down weights computation (aux)
computeUPW	Up weights computation
computeUPW_aux	Up weights computation (aux)
compute_weights_default	Compute default weights
corrplot_from_mutational_matrix	Correlation plot from mutational matrix
corrplot_genes	Gene based correlation plot
corrplot_samples	Sample based correlation plot
dataset_preprocessing	Run CIMICE preprocessing
dataset_preprocessing_population	Run CIMICE preprocessing for poulation format dataset
draw_ggraph	ggplot graph output
draw_networkD3	NetworkD3 graph output
draw_visNetwork	VisNetwork graph output (default)
example_dataset	Creates a simple example dataset
example_dataset_withFreqs	Creates a simple example dataset with frequency column
finalize_generator	Finalize generator normalizing edge weights
fix_clonal_genotype	Manage Clonal genotype in data
format_labels	Format labels for output object
gene_mutations_hist	Histogram of genes' frequencies
get_no_of_children	Get number of children
graph_non_transitive_subset_topology	Default preparation of graph topology
make_dataset	Dataset line by line construction: initialization
make_generator_stub	Create a stub for a generator
make_labels	Helper function to create labels
normalizeDWNW	Down weights normalization
normalizeUPW	Up weights normalization
perturb_dataset	Perturbate a boolean matrix
plot_generator	Plot a generator
prepare_generator_edge_set_command	Prepare a command to add edge weights to a generator
prepare_labels	Prepare node labels based on genotypes
quick_run	Run CIMICE defaults
read	Read a "CAPRI" file
read_CAPRI	Read a "CAPRI" file
read_CAPRIpop	Read a "CAPRIpop" file
read_CAPRIpop_string	Read "CAPRIpop" file from a string
read_CAPRI_string	Read "CAPRI" file from a string
read_MAF	Create mutational matrix from MAF file
read_matrix	Read dataset from an R matrix
remove_transitive_edges	Remove transitive edges from an edgelist
sample_mutations_hist	Histogram of samples' frequencies
select_genes_on_mutations	Filter dataset by genes' mutation count
select_samples_on_mutations	Filter dataset by samples' mutation count
set_generator_edges	Add edge weights to a generator
simulate_generator	Create datasets from generators
to_dot	Dot graph output
update_df	Dataset line by line construction: add a sample