Man pages for davismcc/cardelino
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 |
| clone_id | Infer clonal identity of single cells |
| colMatch | Column match between two matrices by minimum mean absolute... |
| 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 sequencing depths |
| D_input | A matrix of sequencing 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 |
| 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 |
