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Last data update: 2014.03.03

R: The ID Map base class

IdMapBase

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");

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(IdMappingAnalysis)
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.20.0 (2016-02-17) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following objects are masked from 'package:methods':

    getClasses, getMethods

The following objects are masked from 'package:base':

    attach, detach, gc, load, save

Loading required package: rChoiceDialogs
Loading required package: rJava

Attaching package: 'rJava'

The following object is masked from 'package:R.oo':

    clone

This is rChoiceDialogs 1.0.6 2014-09-05
This is IdMappingAnalysis 1.16.0 2013-05-24
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/IdMappingAnalysis/IdMapBase.Rd_%03d_medium.png", width=480, height=480)
> ### Name: IdMapBase
> ### Title: The ID Map base class
> ### Aliases: IdMapBase
> ### Keywords: classes
> 
> ### ** Examples
> 
>  DF<-array(0,dim=c(5,2));
>  obj<-IdMapBase(DF,primaryKey="primary",secondaryKey="secondary");
>  
> 
> 
> 
> 
> dev.off()
null device 
          1 
>