UniquePairs: The UniquePairs class

In IdMappingAnalysis: ID Mapping Analysis

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);

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