gdb.init: Initializes connection with Genomic Database

In misha: Toolkit for Analysis of Genomic Data

Initializes connection with Genomic Database

Description

Initializes connection with Genomic Database: loads the list of tracks, intervals, etc.

Usage

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

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.

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

Value

None.

See Also

gdb.reload, gdb.create, gdir.cd, gtrack.ls, gintervals.ls, gvtrack.ls

misha documentation built on Sept. 14, 2023, 5:08 p.m.