ExpData: Class "ExpData"
In Genominator: Analyze, manage and store genomic data

Description Objects from the Class Slots Details Methods Author(s) See Also Examples

A class for representing experimental data organized along a genome.

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

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..

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.

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.