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()

Arguments

groot

the root directory of the Genomic Database

dir

the current working directory inside the Genomic Database

rescan

indicates whether the file structure should be rescanned

Value

None.

Details

'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.

GROOTRoot directory of Genomic Database
GWDCurrent working directory inside Genomic Database
GTRACKSList of all available tracks
GINTERVSList of all available intervals
GVTRACKSList of all available virtual tracks
ALLGENOMEList of all chromosomes and their sizes
GITERATOR.INTERVALSA set of iterator intervals for which the track expression is evaluated