IdMapBase {IdMappingAnalysis} | R Documentation

## The ID Map base class

### Description

Package: IdMappingAnalysis
Class IdMapBase

`Object`
`~~|`
`~~+--``IdMapBase`

Directly known subclasses:
Bootstrap, Corr, IdMap, IdMapCounts, IdMapDiff, IdMapDiffCounts, JointIdMap, JointUniquePairs, UniquePairs

public static class IdMapBase
extends Object

IdMapBase is an abstract object encapsulating a data frame with at least two columns, the first one (primary) containing character string s identifying the ID under consideration (unprot accessions ID or acc, Entrez Gene ID etc) and the rest of columns containing the variousinformation associated with a given primary ID for a particular DB service.

### Usage

    IdMapBase(DF=NULL, name="", primaryKey=NULL, secondaryKey=NULL, ...)

### Arguments

`DF` | A `data.frame` consisting of two columns (primary and secondary IDs) from which the IdMap object is to be created.
`name` | A `character` string representing the name of the given IdMap object. Default is ”
`primaryKey` | The primary identifier type from which the ID conversion is performed. If `NULL` (default) then the input data frame first column name is used and if it is not available defaults to 'From'.
`secondaryKey` | The secondary identifier type to which conversion is performed. Default is `NULL`.
`...` | Not used.

### Fields and Methods

Methods:

| `[` | -
| `aligned` | Checks if two IdMapBase objects match on column names and primary ID set.
| `as.data.frame` | Retrieves a data frame encapsulated within the given IdMapBase object.
| `dim` | Retrieves dimensions of data frame encapsulated within the given IdMapBase object.
| `dimnames` | Retrieve or set the dimnames of data frame encapsulated within the given IdMapBase object.
| `getName` | Get the name a given IdMapBase object.
| `primaryIDs` | Retrieves the primary IDs for a given IdMapBase object.
| `primaryKey` | Retrieves a primary key for a given IdMapBase object.
| `secondaryKey` | Retrieves a secondary key for a given IdMapBase object.

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save

### Author(s)

Alex Lisovich, Roger Day

### Examples

     DF<-array(0,dim=c(5,2));
     obj<-IdMapBase(DF,primaryKey="primary",secondaryKey="secondary");

[Package IdMappingAnalysis version 1.28.0 Index]