IdMapDiff: The IdMapDiff class

In IdMappingAnalysis: ID Mapping Analysis

Description

Package: IdMappingAnalysis
Class IdMapDiff

Object
~~|
~~+--IdMapBase
~~~~~~~|
~~~~~~~+--IdMapDiff

Directly known subclasses:

public static class IdMapDiff
extends IdMapBase

IdMapDiff constructor implements most time consuming step in comparing two DBs and the structure itself stores the results in a compact form. The IdMapDiff object encapsulates a data.frame the first column of which contains the primary IDs and the rest of columns contain a disjoint representation of the ID Map pair in the form of 3 columns <A-A*B,A*B,B-A*B>, where A and B are secondary ID lists for ID Maps A and B. This class is separated from the IdMapDiffCounts in anticipation of being used by various processing pipelines in a future.

Usage

IdMapDiff(idMap1=NULL, idMap2=NULL, pairNames=c("First", "Second"), verbose=FALSE, ...)

Arguments

idMap1	The first ID Map object on which IdMapDiff object is constructed.
idMap2	The second ID Map object on which IdMapDiff object is constructed.
pairNames	The character vector of length 2 representing the names of the ID Map pair. Default is c('First','Second').
verbose	If TRUE enables diagnostic messages.
...	Not used.

Fields and Methods

Methods:
No methods defined.

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

 #get primary IDs from an msms experiment set
 IDs<-IdMapBase$primaryIDs(examples$msmsExperimentSet);

 #create JointIdMap object aligned by primaryIDs
 jointIdMap<-JointIdMap(examples$identDfList,primaryIDs=IDs);

 # get IdMap list aligned of two ID maps aligned by primaryIDs
 idMaps<-jointIdMap$getIdMapList(verbose=TRUE);

 #create IdMapDiff object
 diffs<-IdMapDiff(idMaps[["NetAffx_F"]],idMaps[["DAVID_Q"]]);
 diffs[1:10,];

 # create IdMapDiff object directly from JointIdMap
 diffs<-jointIdMap$getDiff("NetAffx_F","DAVID_Q",verbose=TRUE);
 

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