comparative single-cell transcriptomics between disease models
and a human condition
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Documentation for package ‘singIST’ version 0.99.85
Help Pages
| add_missing_psb_rows | Ensure all celltype–sample combinations are present in the pseudobulkmatrix |
| asmbPLSDA.cv.kcv | K‐fold × Repeated Cross‐Validation for asmbPLS-DA |
| asmbPLSDA.cv.loo | Leave-one-out Cross-validation |
| biological_link_function | Biological link function |
| calculate_pvalues | Update block of predictor matrices in matrixToBlock() |
| celltype_mapping | Cell type mapping |
| celltype_recap | Derive cell type recapitulation |
| center_scale | Update block of predictor matrices in matrixToBlock() |
| check_fit_model | Validate superpathway fit model |
| check_hyperparameters | Validate asmbPLS-DA hyperparameters |
| check_mapping_organism | Validate mapping organism input |
| check_pathway | Validate pathway fields |
| check_superpathway | Validate superpathway gene sets |
| check_superpathway_input | Check superpathway input for asmbPLS-DA |
| CIP_GIP | Compute Cell Importance Projection (CIP) and Gene Importance Projection (GIP) |
| CIP_GIP_test | Cell and Gene Importance Projections statistical significance |
| clean_mfa_data | Clean a predictor matrix for multiblock MFA |
| compute_final_measures | Update block of predictor matrices in matrixToBlock() |
| compute_IC95 | Update block of predictor matrices in matrixToBlock() |
| compute_permutation_stats | Update block of predictor matrices in matrixToBlock() |
| compute_pvalue | Update block of predictor matrices in matrixToBlock() |
| compute_validation_metrics | Update block of predictor matrices in matrixToBlock() |
| create_fit_model | Create superpathway fit model object |
| create_hyperparameters | Create asmbPLS-DA hyperparameters object |
| create_mapping_organism | Create mapping organism object |
| create_pathway | Create pathway object |
| create_superpathway | Create superpathway gene sets object |
| create_superpathway_input | Create superpathway input for asmbPLS-DA |
| deflate_prediction | Update block of predictor matrices in matrixToBlock() |
| derive_contributions | Derive superpathway score, cell type contribution and gene contribution |
| derive_scores | Compute predictor scores |
| detect_gene_type | Update block of predictor matrices in matrixToBlock() |
| diff_expressed | Compute differentially expressed genes with FindMarkers/findMarkers and descriptive point estimates of log2FC |
| evaluate_performance | Update block of predictor matrices in matrixToBlock() |
| evaluate_quantile_combinations | Update block of predictor matrices in matrixToBlock() |
| execute_parallel_cv | Update block of predictor matrices in matrixToBlock() |
| execute_sequential_cv | Update block of predictor matrices in matrixToBlock() |
| FCtoExpression | Update block of predictor matrices in matrixToBlock() |
| fitOptimal | Cross validation and fit of asmbPLSDA |
| fit_mfa_imputer | Fit a multiblock‐MFA imputer on training data |
| fit_permuted_model | Update block of predictor matrices in matrixToBlock() |
| generate_null_distributions | Update block of predictor matrices in matrixToBlock() |
| gene_contrib | Derive gene contribution to cell type recapitulation |
| get_indices | Update block of predictor matrices in matrixToBlock() |
| get_measure_index | Update block of predictor matrices in matrixToBlock() |
| get_train_val_sets | Update block of predictor matrices in matrixToBlock() |
| helpers | Update block of predictor matrices in matrixToBlock() |
| initialize_results | Update block of predictor matrices in matrixToBlock() |
| jackknife_CIP_GIP | Update block of predictor matrices in matrixToBlock() |
| matrixToBlock | Build predictor and response blocks with superpathway input |
| multiple_check | Check if parameter format is consistent |
| multiple_fitOptimal | Multiple Cross validation and fit of asmbPLSDA |
| multiple_singISTrecapitulations | Compute singIST recapitulations for multiple superpathways |
| orthology_mapping | Orthology mapping |
| performance_measures | Update block of predictor matrices in matrixToBlock() |
| perform_cv | Update block of predictor matrices in matrixToBlock() |
| permute_X_matrix | Update block of predictor matrices in matrixToBlock() |
| permute_Y_matrix | Update block of predictor matrices in matrixToBlock() |
| permut_asmbplsda | Permutation test for asmbPLSDA global significance for LOO |
| permut_asmbplsda_kcv | Permutation test for asmbPLS-DA global significance (LOO or KCV) |
| predict_mfa_imputer | Impute new samples using a fitted MFA imputer |
| pullGeneSet | Pull Gene Set from MsigDB |
| quantile_computation | Update block of predictor matrices in matrixToBlock() |
| render_multiple_outputs | Render multiple singISTrecapitulation outputs |
| restore_removed_columns | Restore columns removed during MFA cleaning into the imputed matrix |
| Results_comparison_measure | Compute performance metrics of predicted asmbPLSDA |
| retrieve_one2one_orthologs | Update block of predictor matrices in matrixToBlock() |
| select_optimal_PLS | Update block of predictor matrices in matrixToBlock() |
| select_samples | Update block of predictor matrices in matrixToBlock() |
| setGeneSetsCelltype | Set gene sets per cell type in a superpathway |
| singISTrecapitulations | Compute singIST recapitulations |
| singIST_treat | Derive singIST treated samples |
| subsampling_CIP_GIP | Update block of predictor matrices in matrixToBlock() |
| superpathway_recap | Derive superpathway recapitulation |
| update_block | Update block of predictor matrices in matrixToBlock() |
| update_group_sizes | Update block‐size vector after cleaning |
| wilcox_CIP_GIP | Mann-Whitney Wilcoxon test p-value |