JointUniquePairs: The JointUniquePairs class
In IdMappingAnalysis: ID Mapping Analysis

Description Usage Arguments Fields and Methods Author(s) Examples

Package: IdMappingAnalysis
Class JointUniquePairs

Object
~~|
~~+--IdMapBase
~~~~~~~|
~~~~~~~+--JointUniquePairs

Directly known subclasses:

public static class JointUniquePairs
extends IdMapBase

UniquePairsMatch object encapsulates a data frame the first two columns of which contain the unique pairs corresponding to the merge (union) of all ID Maps in consideration while the rest of columns contains the match (logical value) between the merged unique pairs set and a unique pairs set specific to the particular ID Map ('d8', 'enV', 'netAffx' etc), one column per Id Map. Used in combination with correlation related data objects (CorrData, Corr, Mixture etc.) to aid in on-fly processing related to some classification by a particular match group The UniquePairsMatch constructor creates an object from the UniquePairs and an ID Map list computing the match (inclusions) for each particular ID Map.

1	JointUniquePairs(uniquePairs=NULL, idMapList=NULL, name="", verbose=FALSE, ...)

`uniquePairs`	UniquePairs object on which a UniquePairsMatch is created or a `data.frame` complying with the UniquePairs class internal data frame format. In case the UniquePairs object is used as a first argument, it's typically obtained from the JointIdMap object by invoking JointIdMap$getUnionIdMap())
`idMapList`	the list of ID Maps on which the match is performed during the UniquePairsMatch object creation The idMapList typically obtained through the call to the JointIdMap.getIdMapList() of the same JointIdMap object as for the first argument to ensure that both arguments are properly aligned.
`name`	A `character` string representing the name of the given IdMap object. Default is ”
`verbose`	If `TRUE` enables diagnostic messages. Default is `FALSE`.
`...`	Not used.

Methods:

	`boxplot`	Draw a basic boxplot based on a given JointUniquePairs object and external data.
	`corr.boxplot`	Boxplot of correlations by match group.
	`corr.plot`	Plot the density distributions for a set of correlation objects .
	`do.glm`	Compute linear regression for the given set of ID Maps.
	`getBootstrap`	Create Bootstrap object from JointUniquePairs object and two experiment sets.
	`getCorr`	Extract a set of correlation objects from given JointUniquePairs object .
	`getCorrData`	Create CorrData object from the JointUniquePairs object and two experiment sets.
	`getCorrDataFrame`	Merge JointUniquePairs and Corr objects into a single data frame.
	`getMapNames`	Get the names of UniquePairs objects encapsulated within the given JointUniquePairs object.
	`getMatchInfo`	Get match table(s) for a given set of primary IDs.
	`getMixture`	Extract mixture model object from JointUniquePairs and Corr objects.
	`getUniquePairs`	Extract the unity UniquePairs object from a given JointUniquePairs object.
	`interactive.corr.boxplot`	Interactive boxplot of correlations by match group.
	`interactive.corr.plot`	Interactive plot of correlation densities.
	`interactive.mixture.boxplot`	Interactive boxplot of mixture component probabilities by match group.
	`interactive.mixture.plot`	Interactive plot of mixture model components.
	`interactive.plot`	General purpose JointUniquePairs interactive plot function.
	`mixture.boxplot`	Boxplot of a mixture model component by match group.
	`mixture.plot`	Plot the correlation densities of the empirical fit, mixture fit and each .
	`subsetCorr`	Subset the Corr object.
	`subsetData`	Subset data on a UniquePairsMatch object.
	`subsetGroups`	Get a JointUniquePairs subset.

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

Alex Lisovich, Roger Day

 #create JointIdMap
 jointIdMap<-JointIdMap(examples$identDfList);

 #creaate unique pairs from the union of all IdMaps within JointIdMap
 pairs<-as.UniquePairs(jointIdMap$getUnionIdMap(verbose=TRUE),verbose=TRUE);

 #create JointUniquePairs object
 jointPairs<-JointUniquePairs(pairs,jointIdMap$getIdMapList(),verbose=TRUE);
 jointPairs[1:10,];