Man pages for pengminshi/cFIT
cFIT (common Factor Space Integration & Transfer)
| ari | Adjusted Rand Index |
| asign_labels | Assign labels for each cell in for target data given the... |
| calculate_alignment | Calculate the alginment score |
| calculate_alignment_per_type | Calculate the alginment score |
| CFITIntegrate | Integration of multiple data source. |
| CFITIntegrate_sketched | Integration of multiple data source by fast cFIT with... |
| CFITTransfer | Transfer the learned gene expression signature onto a new... |
| generate_centers_uniform | Generate gaussian centers with fixed minimum separation c |
| generate_data | Simulate data from the cFIT model |
| get_cluster_match | Map cell labels for each cell type for target data given the... |
| getmode | Get the the mode in a categorical vector |
| gg_color_hue | Generate the defult colors |
| human_gene_to_mouse_genes | Find the mapped mouse gene of each human gene |
| initialize_params | Initialize parameters for data integration or transfer |
| initialize_params_random | Random paramter initialization |
| label_to_membership | Convert label vector to membership matrix |
| logmsg | Log message |
| log_to_both | Log the message to both file and console |
| log_to_console | Log the message to console |
| log_to_file | Log the message to file |
| match_human_expr_to_mouse_genes | Match the human gene expressions to the mouse gene... |
| match_mouse_expr_to_human_genes | Match the mouse gene expressions to the human gene... |
| mouse_gene_to_human_genes | Find the mapped human gene of each mouse gene |
| objective_func | Calculate the objective function |
| plotContTable | Plot the confution matrix |
| plot_umap | UMAP plot |
| preprocess_for_integration | Preprocess expression matrix as input for data integration |
| preprocess_for_transfer | Preprocess expression matrix as input for data transfer |
| select_genes | Select highly variabel genes shared among datasets |
| set_log_level | Set the log threshold |
| solve_b | Solve for dataset specific shift b |
| solve_b_penalized | Solve for dataset specific shift b with Stochastic Porximal... |
| solve_H | Solve for factor loading paramters H |
| solve_lambda_list | Solve for dataset specific scalings lambda.list |
| solve_lambda_list_penalized | Solve for dataset specific scalings lambda.list with... |
| solve_subproblem | Solve subproblems via coordinate descent, given the parameter... |
| solve_subproblem_penalized | Solve subproblems via coordinate descent with Stochastic... |
| solve_W | Solve for nonnegative common factor matrix W |
| solve_W_penalized | Solve for nonnegative common factor matrix W with Stochastic... |
| split_dataset_by_batch | Split the expression matrix into a list of per batch... |
| statistical_leverage_score | Calculate the statistical leverage score |
| step_size | Step size controller |
| subsample | Subsample from a list of data matrix |
| transfer_objective_func | Calculate the objective function |
| transfer_solve_lambda | Solve for dataset specific scalings lambda for target data |
| transfer_solve_subproblem | Solve subproblems via coordinate descent, given the parameter... |
