CorrData {IdMappingAnalysis} | R Documentation

## CorrData class

### 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);

[Package IdMappingAnalysis version 1.24.0 Index]