Man pages for ss-lab-cancerunit/SpiderSeqR
A Tool for Integration of Big Bio Data
| addMissingSamples | Add missing samples from GSEs and SRPs within a data frame |
| classifyAccession | Classify accessions |
| convertAccession | Convert between accession types |
| convertCategoriesToLibraryStrategyType | Convert from SRA-GEO Categories |
| dot-appendGSEColumns | Append information from GSE columns to a data frame |
| dot-batchedAccSearch | Make batched queries to databases |
| dot-checkCondition | Check Condition |
| dot-checkDBFile | Check and ensure that the DB file is in place |
| dot-checkFileDate | Check if DB file is in date (based on metaInfo timestamp) |
| dot-checkValidColumns | Check if column names of df are within allowed set |
| dot-chExtractor | Extract characteristics from a vector |
| dot-clearUpDBFiles | Remove new files |
| dot-convertPairedEnds | Convert the entries to give information about paired ends |
| dot-countAccessionMatches | Count accession matches within a data frame |
| dot-createCustomDBFile | ===*=== ————- Create custom database file |
| dot-createDemoGEO | Create a DEMO GEO database |
| dot-createDemoSRA | Create a DEMO SRA database |
| dot-createDemoSRR_GSM | Create a DEMO SRR_GSM database |
| dot-createFtsTable | Create a new table in a dabase to enable fulltext search... |
| dot-createMockCustomDB | Create a mock custom database file (for use in testing) |
| dot-createMockGEO | Create a mock GEO database file (for use in testing) |
| dot-createMockSRA | ————- ===*==== Suggested names: createMockSRA... |
| dot-createSpiderMetaInfo | Create metaInfo table for SpiderSeqR database |
| dot-cwt | Write table with set parameters |
| dot-detectControls | Detect controls in a sample sheet |
| dot-detectInputs | Detect inputs in a sample sheet |
| dot-detectMerges | Detect merges in a sample sheet |
| dot-extractGSM | Extract GSM from the SRA_experiment_title column |
| dot-filterSRAByTermByAccessionLevel | Filter df according to query matches only within accession... |
| dot-findAccessionLevelColumnNames | Find column names corresponding to accession levels in SRA... |
| dot-findDBFiles | Functions: - .findDBFiles - .missingFileCheck -... |
| dot-findDBFiles_Ori | Find database files |
| dot-findFiles | Find files (a wrapper around list.files) |
| dot-findFiles_Ori | Find files (wrapper around dir allowing to search a few... |
| dot-findSRAAccessionLevelColumnNames | Find SRA column names corresponding to accession levels (ORI) |
| dot-generateCallRecord | Generate record of the call |
| dot-generateDBExtract | Generate DB extract |
| dot-generateEmptyDF | Generate empty df with columns corresponding to database... |
| dot-generateFileName | Generate a file name |
| dot-generateFileName_Accession | Generate a file name (Accession) |
| dot-generateFileName_CALL_SA | Generate file name for call record (searchAnywhere) |
| dot-generateFileName_CALL_SFA | Generate call file for searchForAccession |
| dot-generateOutput | Generate File Output |
| dot-generateOutput_Accession | Generate File Output (Accession) |
| dot-generateParameterRecord | Generate a record of parameters |
| dot-generateSampleSheet_ChIP | Generate ChIP sample sheet |
| dot-generateSampleSheet_Other | Generate 'other' sample sheet |
| dot-generateSampleSheet_RNA | Generate RNA sample sheet |
| dot-generateUniversalSampleSheet | Generate a sample sheet (universal function) |
| dot-getFurtherDBInfo | Get futher database information (metaInfo) |
| dot-listGSEFields | List all column names of the GSE table |
| dot-listGSMFields | List all column names of the GSM table |
| dot-listSRAFields | List all column names of SRA table |
| dot-manageColumns | Manage columns within a data frame |
| dot-manageLibraryStrategy | Manage Library Strategy Formats |
| dot-missingFileCheck | Check for missing files |
| dot-mm | Console Messages |
| dot-noDBFile | Course of action to follow if a db file is missing |
| dot-orderDFColumns | Order columns in a data frame |
| dot-parQuery | Parametrised query for .verifyMissingRuns() |
| dot-progressBar | Generate a progress bar scaled by width |
| dot-rbindUniqueCols | Bind unique entries from two dfs disregarding some of the... |
| dot-renameGSEColumns | Rename df columns derived from gse table to 'GSE_' |
| dot-renameGSMColumns | Rename df columns derived from gsm table to 'GSM_' |
| dot-renameOTHColumns | Rename non-SRA/GEO columns to 'OTH_' |
| dot-renameSRAColumns | Rename df columns derived from sra table to 'SRA_' |
| dot-replaceForbiddenCharacters | Replace forbidden characters from a string |
| dot-saExtractor | Extract sample attributes |
| dot-searchAnywhereGEO | Search anywhere within gse and gsm tables of GEO database |
| dot-searchAnywhereGSE | Search anywhere within gse table of GEO database |
| dot-searchAnywhereGSM | Search anywhere within gsm table of GEO database |
| dot-searchAnywhereSRA | Fulltext search in SRA |
| dot-searchForAccessionAcrossDBsDF | Search for accession across databases |
| dot-searchForSRPChildren | Search for missing SRRs within SRPs |
| dot-searchGEOForGSE | Search for GSE in GEO |
| dot-searchGEOForGSM | Search for GSM in GEO |
| dot-searchSRA | An internal function for searchForTerm |
| dot-searchSRAForAccession | Search for SRA accessions |
| dot-searchSRR_GSM | Search within SRR_GSM database |
| dot-setDBConnections | Set database connections |
| dot-setExpiryParameters | Set expiry parameters |
| dot-tmenu | Some function that will use .tmenu Menu function with testing... |
| dot-unifyDFFormat | Unify formats of data frames |
| dot-unifyNAs | Unify handling of NA values |
| dot-universalExtractor | Universal function for extracting from strings |
| dot-verifyColumns | Verify columns within a data frame |
| dot-verifyConditions | Verify whether conditions are met in a data frame |
| dot-verifyMissingRuns | Verify missing Runs |
| dot-verifySimpleConditions | Verify matches to regular expressions |
| dot-verifySuperseries | Verify presence of superseries |
| dot-vex | Assign local variables to global environment (development... |
| dot-withOut | Remove matching elements from vector |
| dot-writeQuery | Automate Writing SQLite Queries |
| dot-writeTableToFile | Write table to database file |
| dot-writeTableToFile_Ori | Write table to database file |
| filterByTerm | Filter data frame by term |
| filterByTermByAccessionLevel | Filter df according to query matches only within accession... |
| getColumnDescriptions | Get Descriptions of Columns within Databases |
| getDatabaseInformation | Get summaries of database contents |
| getSpiderSeqROption | Inspect the value of package options |
| gse_demo | DEMO extract from gse table (from sqlite file of GEOmetadb... |
| gsm_demo | DEMO extract from gsm table (from sqlite file of GEOmetadb... |
| listColumnSets | Sets of column names for use in display or filtering |
| listValidColumns | List valid columns within the data frames |
| orderAccessions | Order Accessions |
| orderDFAccessions | Order df rows in accession order |
| pipe | Pipe operator |
| rerunSpiderSeqR | Rerun SpiderSeqR query |
| searchAnywhere | Search Anywhere within SRA and GEO databases |
| searchForAccession | Search for Accessions |
| searchForTerm | Search for samples matching criteria of interest |
| selectColumns | Select columns from a data frame |
| selectColumns_Accession | Select columns with accession information |
| selectColumns_Overview | Select columns with overview of sample information |
| setSpiderSeqROption | Set options for functioning of the package |
| SpiderSeqREnv | Environment with default values of the package options |
| SpiderSeqR-package | SpiderSeqR: a tool for integration of SRA and GEO metadata |
| sra_demo | DEMO extract from sra table (from sqlite file of SRAdb... |
| SRA_GEO_Category_Conversion | SRA - GEO Category Conversion Table |
| srr_demo | DEMO extract from srr_gsm table (from custom sqlite database) |
| startSpiderSeqR | Prepare the environment to run SpiderSeqR |
| startSpiderSeqRDemo | Prepare the environment to run SpiderSeqR in DEMO mode |
| testSpiderSeqRConnections | Test SpiderSeqR Connections |
