CorrData: CorrData class

In IdMappingAnalysis: ID Mapping Analysis

Description

Package: IdMappingAnalysis
Class CorrData

Object
~~|
~~+--CorrData

Directly known subclasses:

public static class CorrData
extends Object

CorrData object stores the pair of experiments on which the correlation related processing is performed (MS/MS and mRNA for example) in such a way that two experiments are aligned by experiment names and by the primary keys ensuring the fast correlations. Typically, the primary ID of the ID Map set under consideration is a primary key for a first experiment, and the secondary ID if the ID Map set is a primary key for a second experiment. The alignment of two experiments by primary keys is guaranteed by using the unique pairs object to produce a matching pair of primary keys on which both experiments are ordered. Represented by a list of two elements with names corresponding to the primary and secondary IDs of the unique pairs ('acc' and 'probeset' for example), each element containing a data frame with primary or secondary IDs in the first column while the rest of columns contain the experiment data. The names of the data columns in both data frames are identical and correspond to the sample IDs. The match of sample IDs and an alignment by primary/secondary IDs is ensured by the proper processing during the object creation.

Usage

CorrData(uniquePairs=NULL, expSet1=NULL, expSet2=NULL, verbose=FALSE, ...)

Arguments

uniquePairs	UniquePairs object or a list of such objects on which a single or a list of CorrData objects is constructed.
expSet1	a first ExperimentSet object with primary IDs corresponding (partially intersecting) with the content the first column of UniquePairs (uniquePairsData) object.
expSet2	a second ExperimentSet object with primary IDs corresponding (partially intersecting) with the content the second column of UniquePairs (uniquePairsData) object.
verbose	if TRUE enables diagnostic messages. Default is FALSE.
...	Not used.

Fields and Methods

Methods:

	as.MultiSet	Convert CorrData object into MultiSet object.
	getExperimentSet	Get experiment set data frame for a given modality.
	getSampleNames	Get experiment sample names.
	getUniquePairs	Extract unique pairs from the CorrData object.
	interactive.plot	Draw a scatterplot of experiment data interactively.
	plot	Scatterplot of experiment data.
	primaryKey	Retrieves a primary key for a given CorrData object.
	secondaryKey	Retrieves a secondary key for a given CorrData object.

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

 corrData<-CorrData(examples$uniquePairs,
		examples$msmsExperimentSet,examples$mrnaExperimentSet,verbose=TRUE);
 class(corrData);
 

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