CIMICE                  CIMICE Package
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
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_CAPRI_string       Read "CAPRI" file from a string
read_CAPRIpop           Read a "CAPRIpop" file
read_CAPRIpop_string    Read "CAPRIpop" 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
