IdMapBase: The ID Map base class

In IdMappingAnalysis: ID Mapping Analysis

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");
 

IdMappingAnalysis documentation built on Oct. 31, 2019, 3:30 a.m.