IdMap: The ID Map class

In IdMappingAnalysis: ID Mapping Analysis

Description

Package: IdMappingAnalysis
Class IdMap

Object
~~|
~~+--IdMapBase
~~~~~~~|
~~~~~~~+--IdMap

Directly known subclasses:

public static class IdMap
extends IdMapBase

IdMap is an object encapsulating a data frame with two columns (Primary ID and Secondary ID) where primaryID is a character string uniquely identifying the ID under consideration (unprot accessions ID or acc, Entrez Gene ID etc) and the Secondary ID is a comma separated list of secondary IDs associated with a given primary ID for a particular DB service. The analysis typically starts from obtaining a set of ID Maps (from the various DB services) which are not assumed to have the same number of rows or the same set of primary IDs. The process of alignment of this ID Maps is performed within the JointIdMap

Usage

IdMap(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 IdMap object is to be created.
name	A character string representing the name of the given IdMap object. Default is ”
primaryKey	The name of the primary (first) column in an ID Map. 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	-
	as.UniquePairs	Create a UniquePairs object from a given IdMap object.
	as.list	Coerce an object or a list of compatible object .
	getCounts	Compute the count of secondaryIDs for each primary ID.
	merge	Merge the IdMap object with a second IdMap object or a list of IdMap objects.
	swapKeys	Swap the primary and secondary key columns.

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

 obj<-IdMap(examples$identDfList[[2]]);
 obj$primaryKey();
 obj$secondaryKey();
 

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