attach_dbGaP: Attach dbGaP metadata to a SummarizedExperiment object

In waldronlab/HMP16SData: 16S rRNA Sequencing Data from the Human Microbiome Project

Attach dbGaP metadata to a SummarizedExperiment object

Description

The National Center for Biotechnology Information (NCBI) database of Genotypes and Phenotypes (dbGaP) has extensive metadata pretaining to the HMP study. Access to this metadata is controlled and its use requires authorization by the appropriate Data Access Committee – further information is available here. Those with authorization will be able to download a dbGaP repository key and can use it to attach the controlled-access metadata to a SummarizedExperiment-class object with a single command, provided the NCBI SRA Toolkit is installed and on the user's PATH. See note below for further information.

Usage

attach_dbGaP(x, dbGaP_repository_key = "")

Arguments

x	A SummarizedExperiment-class object from the HMP16SData package
dbGaP_repository_key	A repository key downloaded from dbGaP; only required for the initial download and not needed thereafter

Value

A SummarizedExperiment-class object with protected metadata from dbGaP attached

Note

The NCBI SRA Toolkit is called internally and must be on the user's PATH or an error message will be displayed. The NCBI SRA Toolkit can readily be installed on multiple platforms following these instructions.

See Also

dictionary

Examples

## Not run: 
V13() %>%
    attach_dbGaP(dbGaP_repository_key = "~/prj_12146.ngc")

## End(Not run)

waldronlab/HMP16SData documentation built on Nov. 4, 2024, 7:50 a.m.