Initializes connection with Genomic Database: loads the list of tracks, intervals, etc.
gsetroot(groot = NULL, dir = NULL, rescan = FALSE)
gdb.init(groot = NULL, dir = NULL, rescan = FALSE)
gdb.init_examples()the root directory of the Genomic Database
the current working directory inside the Genomic Database
indicates whether the file structure should be rescanned
None.
'gdb.init' initializes the connection with the Genomic Database. It is typically called first prior to any other function. When the package is attached it internally calls to 'gdb.init.examples' which opens the connection with the database located at 'PKGDIR/trackdb/test' directory, where 'PKGDIR' is the directory where the package is installed.
The current working directory inside the Genomic Database is set to 'dir'. If 'dir' is 'NULL', the current working directory is set to 'GROOT/tracks'.
If 'rescan' is 'TRUE', the list of tracks and intervals is achieved by rescanning directory structure under the current current working directory. Otherwise 'gdb.init' attempts to use the cached list that resides in 'groot/.db.cache' file.
Upon completion the connection is established with the database. If
auto-completion mode is switched on (see 'gset_input_method') the list of
tracks and intervals sets is loaded and added as variables to the global
environment allowing auto-completion of object names with <TAB> key. Also a
few variables are defined at an environment called .misha, and can be
accessed using .misha$variable, e.g. .misha$ALLGENOME.
These variables should not be modified by user.
| GROOT | Root directory of Genomic Database |
| GWD | Current working directory inside Genomic Database |
| GTRACKS | List of all available tracks |
| GINTERVS | List of all available intervals |
| GVTRACKS | List of all available virtual tracks |
| ALLGENOME | List of all chromosomes and their sizes |
| GITERATOR.INTERVALS | A set of iterator intervals for which the track expression is evaluated |