Man pages for jameslhao/dbgapr_dev
A dbGaP Phenotype Data Organizer

accInfoDisplay 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-classBase class of dbgapr package
commons_internalMethod container
commons_publicMethod container
composeFileInfoJson(internal) Construct a data-frame of the phenotype file info...
composeObjAccCompose 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-packagedbgapr: 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
ftpDownloadDownload supplemental data files from dbGaP ftp
getAllDatasetInfoGet meta-info of all datasets
getAllStudyInfoGet 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
getIdInfoGet subject, sample, or pedigree information.
getMetaByObjAccGet metadta of a dbGaP object
getPrjDirGet user project directory
getStudyDatasetInfoGet meta-info of study datasets
getStudyVariableDataGet study variable data by accession
getStudyVariableInfoGet meta-info of study variables
getStudyVariableInfoByDataType(internal) Get meta-info of study numeric or categorical...
getStudyVariableInfoByTermsSearch 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-methodInitialize class Commons
initialize-Study-methodInitialize Study class
isStudyAcc(internal) Validate the format of a dbGaP study accession
manageArchive(internal) Logging archive manager
mergeDatasetConsentMerge 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...
parseIdsFromPhtAccParse ids from dbGaP dataset accession
parseIdsFromPhvAccParse ids from dbGaP variable accession
parseIdsFromStAccParse ids from dbGaP study accession
parsePhenoFileMeta(internal) Parse dataset file info
parsePhtHeaderFromFile(internal) Parse phenotype data file header
prepareDataCopy and preprocess data files
prjConfigCreate user project directory
recordPrjFileInfoExtract and save phenotype file meta-info
saveGapPlot(internal) Save dbGaP data plot to file
searchCopyPhenoFilesCopy phenotype files to project directory
show-Commons-methodDisplay all class Commons methods
show-Study-methodDisplay class methods
stripColNameAcc(internal) Remove accession from concatenated string of...
Study-classClass Study
study_internalMethod container
study_publicMethod container
variableBoxplotVariable boxplot
variableCorrelHeatmapVariable correleation heatmap
variableHistogramVariable histogram
variablePiechartCategorical variable subject count pie-chart
variableScatterplotVariable scatter-plot
variableSummaryVariable data summary
variableVenndiagramSubject 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
jameslhao/dbgapr_dev documentation built on Aug. 15, 2017, 11:22 p.m.