Man pages for jameslhao/dbgapr_dev
A dbGaP Phenotype Data Organizer
| accInfo | Display meta-info of dbGaP objects |
| buildVarCodeValCombo | (internal) Compose variable code-value combo string. |
| checkInputPath | (internal) Validate input directory or file path |
| checkObjStudyByAcc | (internal) Get study of a dataset or variable |
| checkPhvAccList | (internal) Validate variable accessions |
| cleanObjAcc | (internal) Validate the format of dbGaP object |
| Commons-class | Base class of dbgapr package |
| commons_internal | Method container |
| commons_public | Method container |
| composeFileInfoJson | (internal) Construct a data-frame of the phenotype file info... |
| composeObjAcc | Compose dbGaP object accession |
| convertEnumVarColName | (internal) Convert enumerated integer type variable value |
| copyUserFile | (internal) Copy decrypted dbGaP files to user project... |
| createPrjDir | (internal) Create user project directory |
| dataDicXmlParser | (internal, deprecated) XML parser of the data dictionary file |
| dbgapr-package | dbgapr: A dbGaP Phenotype Data Organizer |
| detectVariableDataType | (internal, deprecated) Detect variable data type |
| displayTable | (internal) Display text file content |
| displayTextFile | (Internal) Display text file content |
| filterBySubjIds | (internal) Filter dataset data by subject ids |
| ftpDownload | Download supplemental data files from dbGaP ftp |
| getAllDatasetInfo | Get meta-info of all datasets |
| getAllStudyInfo | Get meta-info of all studies |
| getAvailPhtVer | (internal) Get available dataset accession by variable... |
| getDataDicByStudy | (internal) Get study variable meta-info (data dictionary) |
| getDatasetDataByPhtAcc | (internal) Get data by dataset accession |
| getDatasetMetaByStudy | (internal) Get study variable meta-info (data dictionary) |
| getExtData | (internal) Get the supplemental (external) data |
| getIdInfo | Get subject, sample, or pedigree information. |
| getMetaByObjAcc | Get metadta of a dbGaP object |
| getPrjDir | Get user project directory |
| getStudyDatasetInfo | Get meta-info of study datasets |
| getStudyVariableData | Get study variable data by accession |
| getStudyVariableInfo | Get meta-info of study variables |
| getStudyVariableInfoByDataType | (internal) Get meta-info of study numeric or categorical... |
| getStudyVariableInfoByTerms | Search variables by terms |
| getVariableDataByPhvAcc | (internal) Get variable data by accession |
| getVariableDataByPhvAccAndSubjId | (internal) Get variable data subset by subject ids |
| getVariableInfoByPhvAcc | (internal) Get variable meta-info by accession |
| getVarNameAccCombos | (internal) Get concatenated variable name and accession combo... |
| getVarNameByPhvAcc | (internal) Get variable names given accessions |
| initialize-Commons-method | Initialize class Commons |
| initialize-Study-method | Initialize Study class |
| isStudyAcc | (internal) Validate the format of a dbGaP study accession |
| manageArchive | (internal) Logging archive manager |
| mergeDatasetConsent | Merge dataset data of different consents |
| mergeDatasetConsentByStudy | (internal) Merge data of different consent groups in a study |
| parseDataDic | (internal, deprecated) Parse data dictionary XML files of all... |
| parseDataDicByStudy | (internal, deprecated) Parse data dictionary XML files of a... |
| parseIdsFromPhtAcc | Parse ids from dbGaP dataset accession |
| parseIdsFromPhvAcc | Parse ids from dbGaP variable accession |
| parseIdsFromStAcc | Parse ids from dbGaP study accession |
| parsePhenoFileMeta | (internal) Parse dataset file info |
| parsePhtHeaderFromFile | (internal) Parse phenotype data file header |
| prepareData | Copy and preprocess data files |
| prjConfig | Create user project directory |
| recordPrjFileInfo | Extract and save phenotype file meta-info |
| saveGapPlot | (internal) Save dbGaP data plot to file |
| searchCopyPhenoFiles | Copy phenotype files to project directory |
| show-Commons-method | Display all class Commons methods |
| show-Study-method | Display class methods |
| stripColNameAcc | (internal) Remove accession from concatenated string of... |
| Study-class | Class Study |
| study_internal | Method container |
| study_public | Method container |
| variableBoxplot | Variable boxplot |
| variableCorrelHeatmap | Variable correleation heatmap |
| variableHistogram | Variable histogram |
| variablePiechart | Categorical variable subject count pie-chart |
| variableScatterplot | Variable scatter-plot |
| variableSummary | Variable data summary |
| variableVenndiagram | Subject overlapping with Venndigram |
| viewAllDatasetInfo | (internal) Display meta-info of all datasets |
| viewAllStudyInfo | (internal) Display meta-info of all studies |
| viewStudyVariableInfo | (internal) View study variable meta-info |
| writeFileInfoJson | (internal) Write file info json |
| writeLog | (internal) Error Logging |
