A_clone                 A matrix of read numbers of alternative alleles
                        for clone ID
A_germline              A matrix of read numbers of alternative alleles
assign_cells_to_clones
                        Assign cells to clones from cardelino results
assign_scores           Scoring the simulation in assignment of
                        singlets and doublets
binaryPRC               Precision-recall curve for binary label
                        prediction
binaryROC               ROC curve for binary label prediction
Clone ID                Infer clonal identity of single cells
colMatch                Column match between two matrices by minimum
                        mean absolute difference
Config_all              A list of tree configuration
D_clone                 A matrix of sequencing depths for clone ID
D_germline              A matrix of sequencing depths
D_input                 A matrix of sequencing depths
devianceIC              Deviance Information Criterion for cardelino
                        model
donor_read_simulator    Reads simulator for donor identification
get_logLik              Log likelihood of clone_id model It returns
                        P(A, D | C, I, theta0, theta1)
get_snp_matrices        Get SNP data matrices from VCF object(s)
get_tree                Get a clonal tree from a configuration matrix
Geweke_Z                Geweke diagnostic for MCMC sampling.
heat_matrix             Plot heatmap from a matrix
heatmap.theme           The theme of heatmaps for prob_heatmap and
                        sites_heatmap
load_cellSNP_vcf        Load sparse matrices A and D from cellSNP VCF
                        file with filtering SNPs
load_GT_vcf             Load genotype VCF into numeric values: 0, 1, or
                        2
mixBinom                EM algorithm for estimating binomial mixture
                        model
mtx_to_df               Convert a matrix to data frame
multiPRC                Precision-recall curve for multi-class
                        prediction
plot_config_diffs       Define a publication-style plot theme
plot_tree               Plot a phylogenetic tree
predMixBinom            Predicted probability from learned binomial
                        mixture model
prob_heatmap            Plot a heatmap for probability of clone
                        assignment
pub.theme               Define a publication-style plot theme
read_vcf                Read a VCF file into R session
rowArgmax               Column index of the maximum value for each row
                        in a matrix
rowMax                  Maximum value for each row in a matrix
sample_seq_depth        Update matrix D with manually selected missing
                        rate
sample_tree_SNV         Down sample number of SNVs in the tree
sim_read_count          Synthetic reads generator for genetic variants
tree                    A tree object
tree_3clone             A tree object
tree_4clone             A tree object
tree_5clone             A tree object
vc_heatmap              Plot a variant-cell heatmap for cell clonal
                        assignment
