# Clone Identification from Single Cell Data

## Documentation for package ‘cardelino’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

assign_cells_to_clones | Assign cells to clones from cardelino results
assign_scores | Scoring the simulation in assignment of singlets and doublets
A_clone | A matrix of read numbers of alternative alleles for clone ID
A_germline | A matrix of read numbers of alternative alleles
binaryPRC | Precision-recall curve for binary label prediction
binaryROC | ROC curve for binary label prediction
Clone ID | Infer clonal identity of single cells
clone_id | Infer clonal identity of single cells
clone_id_EM | Infer clonal identity of single cells
clone_id_Gibbs | Infer clonal identity of single cells
colMatch | Column match between two matrices by minimum mean absolute difference
Config_all | A list of tree configuration
devianceIC | Deviance Information Criterion for cardelino model
donor_read_simulator | Reads simulator for donor identification
D_clone | A matrix of sequencing depths for clone ID
D_germline | A matrix of sequencing depths
D_input | A matrix of sequencing depths
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.
heatmap.theme | The theme of heatmaps for prob_heatmap and sites_heatmap
heat_matrix | Plot heatmap from a matrix
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