dbgapr-package: dbgapr: A dbGaP Phenotype Data Organizer

In jameslhao/dbgapr_dev: A dbGaP Phenotype Data Organizer

Description

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).

Details

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

jameslhao/dbgapr_dev documentation built on May 8, 2019, 11:03 p.m.