dbgapr is a collection of the functions that help to organize, search, review, and retrieve the phenotype data downloaded from the Database of Genotypes and Phenotypes (dbGaP) sponsored by the National Institutes of Health (NIH).
The main functions of the package are:
Organize downloaded phenotype data files by studies in a central location.
Merge the data files of different consents.
Make data meta-info readily available for search and view.
Query data meta-info and retrieve data by dbGaP object accessions.
Basic plotting for data visualization.
Vignettes
To learn more about dbgapr, start with the vignettes: 'browseVignettes(package = "dbgapr")'
The functions of the package belong to Commons
and Study
two classes. The public functions of the classes are listed below.
Commons class
prjConfig
getPrjDir
prepareData
searchCopyPhenoFiles
ftpDownload
recordPrjFileInfo
mergeDatasetConsent
accInfo
getAllStudyInfo
getAllDatasetInfo
Study class
getStudyDatasetInfo
getStudyVariableInfo
getStudyVariableInfoByTerms
getStudyVariableData
getIdInfo
variableSummary
variableBoxplot
variableScatterplot
variableHistogram
variablePiechart
variableVenndiagram
variableCorrelHeatmap
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