Man pages for Paradigm4/revealgenomics
SciDB REVEAL/Genomics API
| add_user_to_data_loaders | placeholder to be filled in |
| aggr_proj_study_by_pheno | Aggregate project, study info by phenotype column(s) |
| api_register_biosamples | Samples / Biosample |
| api_register_definitions | register definitions for dataset |
| api_register_featuresets_experimentsets_measurementsets | Register FeatureSets, ExperimentSets and MeasurementSets |
| api_register_individuals | register individuals |
| api_register_measurements | Register measurements |
| api_register_ontology_from_definition_sheet | automatically register ontology terms |
| as.scidb_int64_cols | wrapper for as.scidb when supplying int64 types When type... |
| autoconvert_char | Auto-promote characters to types |
| build_reference_gene_set | Build a reference gene set at user specified FeatureSet id |
| calculate_statistics_across_measurementsets | Calculate summary statistics across measurementsets |
| calculate_statistics_across_measurementsets_from_measurementdata_cache | Calculate statistics across all MeasurementSets by consulting... |
| calculate_statistics_rnaquantification | Calculate statistics on Gene-Expression data |
| calculate_statistics_variant | Calculate statistics on Variant data |
| check_if_revealgenomics_dataframes_equal | check if two API results are identical |
| Choices | classes to handle different choices sheets in Excel template |
| convertToExpressionSet | Convert Expression data.frame to ExpressionSet |
| createSpectralMap | Generate SpectralMaps using the first 3 PCs |
| custom_scan | whether to use secure_scan or not |
| DataLoader | download features for current featureset |
| DataLoaderCopyNumberVariantFormatA | loader to try and handle various copy number variant... |
| DataLoaderVariantExomic | assign dataset_id and measurementset_id |
| DataLoaderVariantFormatA | loader to try and handle various variant formats • currently... |
| DataLoaderVariantGemini | loader corresponding to GEMINI files • May need to use... |
| DataReaderCopyNumberVariantVariableColumns | generic variant loader that aims to work with multiple... |
| DataReaderVariantFormatA | generic variant loader that aims to work with multiple... |
| delete_featureset | Delete FeatureSet after checking if used anywhere |
| download_unpivot_info_join | Download from scidb then unpivot info and join in R |
| estimate_measurementdata_download_size | Estimate downloaded size for measurement data |
| feature_matching_level1 | Level 1 feature matching |
| FeaturesetChoices | extract relevant info pertaining to featureset_choices sheet |
| FilterChoices | extract relevant info pertaining to filter_choices sheet |
| filter_on_dataset_id_and_version | internal function for 'search_METADATA()" |
| find_dataset_id_by_grep | Returns dataset_ids by grep on name |
| find_dataset_id_by_metadata_value | Find matching datasets by searching across entities |
| find_matches_and_return_indices | helper function to report matches between vectors |
| find_matching_featureset | find featureset from Pipeline sheet info |
| find_project_id_by_grep | Returns project_ids by grep on name |
| flexible_mpm | Principal component analysis of a matrix |
| formulate_build_literal_query | Formulate query to build array from vector |
| formulate_cell_population_data_tree_from_features_dataframe | Formulate data tree from CyTOF feature data.frame |
| formulate_feature_source_from_measuremenset | Formulate feature source string for use in feature... |
| formulate_versioned_selection_query | Add version filter on top a filter string |
| full_arrayname | full name of array with namespace |
| get_entity_from_cache | get_ENTITY for cached entities |
| get_entity_from_entity_id | Get entity name |
| get_entity_id | Get entity id |
| get_entity_infoArrayExists | does infoArray exist for given entity |
| get_experiments | retrieve all the experiments available to logged in user |
| get_genelist_gene_symbols | Gene list gene symbols visible to user |
| get_individuals | Retrieve individuals |
| get_list_of_arrays | Get list of arrays maintained by revealgenomics API |
| get_logged_in_user | Report logged in user |
| get_mandatory_fields_for_register_entity | mandatory fields (internal function) |
| get_measurements | Retrieve data from 'Measurement' entity |
| grant_initial_access | grant initial access to a user |
| init_db | (potentially delete and) initialize arrays managed by... |
| init_r_object_cache | Initialize R object cache array |
| is_entity_cached | is entity cached |
| join_info | Join flex fields |
| join_info_unpivot | Join flex fields and unpivot |
| lean_esetSpectralMap | plot spectral map biplot of an eSet object |
| list_datasets | list studies |
| list_ncol_in_aux_column | List count of sub-columns per row in a column that is a JSON... |
| list_nrow_in_aux_column | List count of sub-rows per row in a column that is a JSON... |
| list_users | list users registered with scidb |
| load_helper_column_rename | helper function to rename columns |
| load_helper_do_entity_specific_work | Record all entity specific work per entity in one place |
| load_helper_handle_duplicates | Drop duplicate rows before importing |
| load_helper_prepare_dataframe | Wrapper function combining common actions for preparing... |
| load_helper_replace_local_ids | get rid of local indexes |
| mandatory_fields | mandatory fields |
| match_features | convenience function for matching features between database... |
| merge_aux_info_from_df | Get auxiliary information from a dataframe, and merge as JSON... |
| merge_aux_info_from_file | Get auxiliary information from a file, and merge as JSON... |
| myExcelLoader | Load Excel workbook into memory |
| myExcelReader | Read sheet from Excel workbook |
| names_to_numbered_vec_by_uniqueness | names to list of numbers by uniqueness |
| na_to_blank | convert NA to blank |
| PipelineChoices | extract relevant info pertaining to pipeline_choices sheet |
| populate_measurements | register all measurements for all / a specific dataset |
| prep_df_fields | Compare with mandatory fields passed by user |
| pretty_print | Pretty print a large vector of strings, integers etc. |
| register_copynumbervariant_variable_columns | Register CNV data of variable columns subtype |
| register_entities_excel | register entities via Excel sheet |
| register_entities_workbook | register entities via list of R data-frames |
| register_entity_flex_fields | Register info for entities into entity wide array |
| register_expression_dataframe | Upload data into gene expression, protein expression, copy... |
| register_expression_matrix | Upload expression matrix file |
| register_expression_matrix_client | Upload expression matrix file |
| register_features_from_gtf_file | Register features from GTF file |
| register_features_from_gxf_file | Register features from GTF/GFF3 file |
| register_genelist | Register genelist |
| register_genelist_gene | Register gene symbols in a gene-list |
| register_gene_symbol | register gene_symbols |
| register_in_memory_matrix | Register in-memory matrix |
| register_mandatory_and_flex_fields | Register the mandatory fields and update lookup |
| register_r_object_at_key | Upload an R object at key |
| remove_old_versions_for_entity | remove old array versions associated with an entity |
| remove_versions | remove old versions associated with an array |
| retrieve_r_object_at_key | Retrieve R object associated with key |
| return_sub_indices | Return sub indices |
| revealgenomics | GA4GH inspired and SciDB backed R API for genomic data |
| run_quality_control_checks | Run QC checks on data loaded via Excel file |
| run_tests_dataframe | Run tests on data frame |
| search_copy_number_variant | Search copy number variant data |
| search_copynumbervariant_variable_columns | Search copy number variant subtype (variable columns) |
| search_expression | Search expression data (RNA-seq / GXP by Microarray,... |
| search_expression_by_one_measurementset_zero_or_more_features | Subpath for 'search_expression' |
| search_expression_by_one_or_more_biosamples | Subpath for 'search_expression' |
| search_feature_by_synonym | Search features by synonym |
| search_features | Search features |
| search_fusion | Search Fusion data |
| search_individuals | Search individuals by dataset |
| search_measurementdata | Unified function to download entire pipeline worth of data |
| search_metadata_attrkey | Search metadata attributes by entity id |
| search_metadata_value | Search metadata value array by values |
| search_ontology_category | Search ontology category by categories |
| search_rnaquantification | Deprecated function to search gene expression data |
| search_variant | search variants |
| search_variants | Deprecated function for searching variant data |
| search_variants_scidb | Inner function for searching variants |
| search_versioned_secure_metadata_entity | internal function for 'search_METADATA()' |
| search_versioned_secure_metadata_entity_by_requested_attributes | internal function for 'search_METADATA()' by set of requested... |
| select_from_1d_entity | internal function for get_METADATA() |
| set_permissions | set per study access permissions for a user |
| show_dataset_permissions | show study permissions |
| show_roles_for_user | Function to show rules for user |
| show_user_permissions | show user permissions |
| template_helper_assign_experiment_entity | Assign experiment entity |
| template_helper_assign_measurement_entity | Assign measurement entity |
| template_helper_convert_names | Convert external (human-readable names) to API internal names |
| template_helper_enforce_columns_defined | Enforce that columns in any data sheet have definitions in... |
| template_helper_enforce_mandatory_columns_present | Enforce that mandatory columns listed in Definitions sheet... |
| template_helper_extract_definitions | extract definitions corresponding to a specific sheet |
| template_helper_extract_pipeline_meta_info | Extract pipeline meta information |
| template_helper_extract_record_related_rows | extract information pertaining to a project-study record |
| template_helper_formulate_file_path | Formulate a file path from Excel template |
| template_helper_suffix_by_entity | Convert entity to suffix |
| template_linker | Storing columns that link different sheets |
| user_confirms_action | check before proceeding |
