emuR (version 2.4.0)

load_emuDB: Load emuDB

Description

Function loads emuDB into its cached representation and makes it accessible from within the current R session by returning a emuDBhandle object

Usage

load_emuDB(
  databaseDir,
  inMemoryCache = FALSE,
  connection = NULL,
  verbose = TRUE,
  ...
)

Value

emuDB handle object

Arguments

databaseDir

directory of the emuDB

inMemoryCache

cache the loaded DB in memory

connection

pass in DBI connection to SQL database if you want to override the default which is to use an SQLite database either in memory (inMemoryCache = TRUE) or in the emuDB folder. This is intended for expert use only!

verbose

be verbose

...

additional parameters

Details

In order to access an emuDB from R it is necessary to load the annotation and configuration files to an emuR internal database format. The function expects a emuDB file structure in directory databaseDir. The emuDB configuration file is loaded first. On success the function iterates through session and bundle directories and loads found annotation files. The parameter inMemoryCache determines where the internal database is stored: If FALSE a database cache file in databaseDir is used. When the database is loaded for the first time the function will create a new cache file and store the data to it. On subsequent loading of the same database the cache is only updated if files have changed, therefore the loading is then much faster. For this to work the user needs write permissions to databaseDir and the cache file. The database is loaded into a volatile in-memory database if inMemoryCache is set to TRUE.

Examples

if (FALSE) {
## Load database ae in directory /homes/mylogin/EMUnew/ae 
## assuming an existing emuDB structure in this directory

ae = load_emuDB("/homes/mylogin/EMU/ae")

## Load database ae from demo data

# create demo data in temporary directory
create_emuRdemoData(dir = tempdir())
# build base path to demo emuDB
demoDatabaseDir = file.path(tempdir(), "emuR_demoData", "ae_emuDB")

# load demo emuDB
ae = load_emuDB(demoDatabaseDir)

}