ExpData-class {Genominator} | R Documentation

## Class "ExpData"

### 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

    showClass("ExpData")

[Package Genominator version 1.36.0 Index]