Man pages for Paradigm4/insight

add_user_to_data_loadersplaceholder to be filled in
aggr_proj_study_by_phenoAggregate project, study info by phenotype column(s)
api_register_biosamplesSamples / Biosample
api_register_definitionsregister definitions for dataset
api_register_featuresets_experimentsets_measurementsetsRegister FeatureSets, ExperimentSets and MeasurementSets
api_register_individualsregister individuals
api_register_measurementsRegister measurements
api_register_ontology_from_definition_sheetautomatically register ontology terms
as.scidb_int64_colswrapper for as.scidb when supplying int64 types When type...
autoconvert_charAuto-promote characters to types
build_reference_gene_setBuild a reference gene set at user specified FeatureSet id
calculate_statistics_across_measurementsetsCalculate summary statistics across measurementsets
calculate_statistics_rnaquantificationCalculate statistics on Gene-Expression data
calculate_statistics_variantCalculate statistics on Variant data
Choicesclasses to handle different choices sheets in Excel template
custom_scanwhether to use secure_scan or not
dao_search_expressionFaster implementation of 'search_expression' for UI...
DataLoaderdownload features for current featureset
DataLoaderVariantFormatAloader to try and handle various variant formats • currently...
DataLoaderVariantGeminiloader corresponding to GEMINI files • May need to use...
DataReaderVariantFormatAgeneric variant loader that aims to work with multiple...
estimate_measurementdata_download_sizeEstimate downloaded size for measurement data
feature_matching_level1Level 1 feature matching
FeaturesetChoicesextract relevant info pertaining to featureset_choices sheet
FilterChoicesextract relevant info pertaining to filter_choices sheet
filter_on_dataset_id_and_versioninternal function for 'search_METADATA()"
find_dataset_id_by_grepReturns dataset_ids by grep on name
find_matches_and_return_indiceshelper function to report matches between vectors
find_matching_featuresetfind featureset from Pipeline sheet info
formulate_versioned_selection_queryAdd version filter on top a filter string
full_arraynamefull name of array with namespace
get_entity_from_cacheget_ENTITY for cached entities
get_entity_infoArrayExistsdoes infoArray exist for given entity
get_experimentsretrieve all the experiments available to logged in user
get_individualsRetrieve individuals
get_logged_in_userReport logged in user
get_mandatory_fields_for_register_entitymandatory fields (internal function)
get_measurementsRetrieve data from 'Measurement' entity
grant_initial_accessgrant initial access to a user
init_db(potentially delete and) initialize arrays managed by...
is_entity_cachedis entity cached
join_infoJoin flex fields
join_info_unpivotJoin flex fields and unpivot
list_datasetslist studies
list_ncol_in_aux_columnList count of sub-columns per row in a column that is a JSON...
list_nrow_in_aux_columnList count of sub-rows per row in a column that is a JSON...
list_userslist users registered with scidb
load_helper_column_renamehelper function to rename columns
load_helper_do_entity_specific_workRecord all entity specific work per entity in one place
load_helper_handle_duplicatesDrop duplicate rows before importing
load_helper_prepare_dataframeWrapper function combining common actions for preparing...
load_helper_replace_local_idsget rid of local indexes
mandatory_fieldsmandatory fields
match_featuresconvenience function for matching features between database...
merge_aux_info_from_dfGet auxiliary information from a dataframe, and merge as JSON...
merge_aux_info_from_fileGet auxiliary information from a file, and merge as JSON...
myExcelLoaderLoad Excel workbook into memory
myExcelReaderRead sheet from Excel workbook
names_to_numbered_vec_by_uniquenessnames to list of numbers by uniqueness
PipelineChoicesextract relevant info pertaining to pipeline_choices sheet
populate_measurementsregister all measurements for a specific dataset
prep_df_fieldsCompare with mandatory fields passed by user
pretty_printPretty print a large vector of strings, integers etc.
register_entities_excelregister entities via Excel sheet
register_entities_workbookregister entities via list of R data-frames
register_expression_dataframeUpload data into gene expression, protein expression arrays
register_expression_matrixUpload expression matrix file
register_expression_matrix_clientUpload expression matrix file
register_genelistRegister genelist
register_genelist_geneRegister gene symbols in a gene-list
register_gene_symbolregister gene_symbols
register_mandatory_and_flex_fieldsRegister the mandatory fields and update lookup
remove_old_versions_for_entityremove old array versions associated with an entity
remove_versionsremove old versions associated with an array
revealgenomicsGA4GH inspired and SciDB backed R API for genomic data
run_tests_dataframeRun tests on data frame
search_expressionSearch expression data (RNA-seq / GXP by Microarray,...
search_feature_by_synonymSearch features by synonym
search_fusionSearch Fusion data
search_individualsSearch individuals by dataset
search_measurementdataUnified function to download entire pipeline worth of data
search_rnaquantificationDeprecated function to search gene expression data
search_variantsearch variants
search_variantsDeprecated function for searching variant data
search_variants_scidbInner function for searching variants
search_versioned_secure_metadata_entityinternal function for search_METADATA()
select_from_1d_entityinternal function for get_METADATA()
set_permissionsset per study access permissions for a user
show_dataset_permissionsshow study permissions
show_user_permissionsshow user permissions
template_helper_convert_namesConvert external (human-readable names) to API internal names
template_helper_enforce_columns_definedEnforce that columns in any data sheet have definitions in...
template_helper_enforce_mandatory_columns_presentEnforce that mandatory columns listed in Definitions sheet...
template_helper_extract_definitionsextract definitions corresponding to a specific sheet
template_helper_extract_pipeline_meta_infoExtract pipeline meta information
template_helper_extract_record_related_rowsextract information pertaining to a project-study record
template_helper_suffix_by_entityConvert entity to suffix
template_linkerStoring columns that link different sheets
Paradigm4/insight documentation built on Dec. 17, 2018, 1:19 p.m.