Clone Identification from Single Cell Data

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 |

cardelino-package | Clone Identification from Single Cell Data |

clone_id | Infer clonal identity of single cells |

colMatch | Column match between two matrices by the minimum mean... |

Config_all | A list of tree configuration |

D_clone | A matrix of sequencing depths for clone ID |

devianceIC | Deviance Information Criterion for cardelino model |

D_germline | A matrix of sequncing depths |

D_input | A matrix of sequncing depths |

donor_read_simulator | Reads simulator for donor identification |

get_logLik | Log likelihood of clone_id model It returns P(A, D | C, I,... |

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... |

load_GT_vcf | Load genotype VCF into numeric values: 0, 1, or 2 |

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 |

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 manully selected missing rate |

sample_tree_SNV | Down sample number of SNVs in the tree |

sim_read_count | Sythetic 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 |

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