UniquePairs {IdMappingAnalysis} | R Documentation

## The UniquePairs class

### Description

Package: IdMappingAnalysis
Class UniquePairs

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

Directly known subclasses:

public static class UniquePairs
extends IdMapBase

The alternative representation of an IdMap suitable for performing the correlation related processing. Contains a data frame with two columns, each row of which represents a unique pair <primary ID, secondary ID> where primary ID corresponds to the primaryIDs of an ID Map and secondary ID corresponds to a single ID from a list of comma separated secondary IDs within the corresponding ID Map. The column names correspond to the primary/secondary keys of an Id Map ('acc' and 'probeset' for example)

### Usage

    UniquePairs(DF=NULL, name="", primaryKey=colnames(DF)[1], secondaryKey=colnames(DF)[2], ...)

### Arguments

`DF` | A `data.frame` consisting of two columns (primary and secondary IDs) from which the UniquePairs object is to be created.
`name` | A `character` string representing the name of the given UniquePairs object. Default is ”
`primaryKey` | The name of the primary (first) column of a `data.frame` encapsulated within the UniquePairs object. If missing then the input data frame first column name is used and if it is not available defaults to 'From'.
`secondaryKey` | The name of secondary (second) column in an ID Map. If missing then the input data frame second column name is used and if it is not available defaults to 'To'.
`...` | Not used.

### Fields and Methods

Methods:

| `as.IdMap` | Convert the UniquePairs object into the IdMap object.
| `as` | -
| `create` | Create a UniquePairs object from a single IdMap or a list of IdMap objects.
| `equals` | Check if two unique pairs data structures are identical.
| `getMatch` | Get the logical vector of pair matches of the given UniquePairs object .
| `swapKeys` | Swap the primary and secondary key columns.
| `unique` | Extract unique elements.

Methods inherited from IdMapBase:
[, aligned, as.data.frame, dim, dimnames, getName, primaryIDs, primaryKey, secondaryKey

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<-matrix(
      c("P25685","200664_s_at",
        "P25685","200666_s_at",
        "Q6ZV71","205208_at",
        "Q6ZV71","215798_at",
        "P05164", "203948_s_at"
      ),ncol=2,nrow=5,byrow=TRUE);
     colnames(DF)<-c("Uniprot","Affy");

     uniquePairs<-UniquePairs(DF);

[Package IdMappingAnalysis version 1.28.0 Index]