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

## Documentation for package ‘CIMICE’ version 1.19.0

- 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