load_emuDB {emuR} | R Documentation |
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,
...
)
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 ( |
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
.
Value
emuDB handle object
Examples
## Not run:
## 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)
## End(Not run)