Class "ExpData"

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Description

A class for representing experimental data organized along a genome.

Objects from the Class

The preferred way to construct objects of class ExpData is to use the constructor function ExpData(dbFilename = "filename.db", tablename = "tablename")

Slots

dbFilename:

A "character" containing the filename of the SQLite database.

tablename:

A "character" containing the tablename of the relevant SQLite table.

indexColumns:

A "character", listing which columns (and in which order) in the table has been indexed.

mode:

A "character" indicating whether the database is in read or write mode. Write mode implies read mode.

chrMap:

A "character" which is a placeholder, for now.

.tmpFile:

A "character". Only for developers..

Details

For all practical purposes, the class may be considered to point to a specific table in an SQLite database. A connection to the database is opened automatically and a pool of connections is maintained.

Methods

ExpData(dbFilename, tablename, mode, indexColumns, pragma)

A constructor function. The last three arguments are for expert users.

getDBConnection

Returns a connection to the database associated with the ExpData object.

getDBFilename

Returns the filename of the database associated with the ExpData object.

getTablename

Returns the tablename of the ExpData object

getSchema

Returns the schema of the table associated with the ExpData object.

getIndexColumns

Returns the indexColumns of the object.

getColnames

Returns all columns (argument all = TRUE) or all columns except the indexColumns (argument all = FALSE).

listTables

Returns all vector of tables in a database.

getMode

Returns the mode of the ExpData object.

[

signature(x = "ExpData"): subsetting of the object. ExpData objects do not have rownames.

$

signature(x = "ExpData"): selects a column of the table.

head

signature(x = "ExpData"): prints the first 10 rows of the object.

initialize

signature(.Object = "ExpData"): The initialize method; use the constructor function ExpData instead.

show

signature(object = "ExpData"): the show method.

Author(s)

James Bullard bullard@berkeley.edu, Kasper Daniel Hansen khansen@jhsph.edu

See Also

The package vignettes.

Examples

1
showClass("ExpData")