colDescriptions: Get column descriptions of SRAmetadb.sqlite
In zhujack/SRAdb: A compilation of metadata from NCBI SRA and tools

colDescriptions

R Documentation

Get column descriptions of SRAmetadb.sqlite

Description

Get column descriptions of SRAmetadb.sqlite, including table, field, field data type, description and default values

Usage

colDescriptions( sra_con )

Arguments

sra_con

Connection of the SRAmetadb SQLite database

Value

A seven-column data.frame including table_name, field_name, type, description, value_list.

Author(s)

Jack Zhu<zhujack@mail.nih.gov> and Sean Davis <sdavis2@mail.nih.gov>

Examples

## Using the SRAmetadb demo database
  
    library(SRAdb)
	sra_dbname <- file.path(system.file('extdata', package='SRAdb'), 'SRAmetadb_demo.sqlite')	
    sra_con <- dbConnect(dbDriver("SQLite"), sra_dbname)
  
    ## Get column descriptions
    a <- colDescriptions(sra_con=sra_con)[1:5,]

## The actual SRAmetadb sqlite database can be downloaded using function: getSRAdbFile. Warning: the actual SRAmetadb sqlite database is pretty large (> 35GB as of May, 2018) after uncompression. So, downloading and uncompressing of the actual SRAmetadb sqlite could take quite a few minutes depending on your network bandwidth. Direct links for downloading the SRAmetadb sqlite database:  https://s3.amazonaws.com/starbuck1/sradb/SRAmetadb.sqlite.gz https://gbnci-abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz

zhujack/SRAdb documentation built on Oct. 26, 2022, 7:32 a.m.