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

Fields and Methods

Methods:

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);
 

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(IdMappingAnalysis)
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.20.0 (2016-02-17) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following objects are masked from 'package:methods':

    getClasses, getMethods

The following objects are masked from 'package:base':

    attach, detach, gc, load, save

Loading required package: rChoiceDialogs
Loading required package: rJava

Attaching package: 'rJava'

The following object is masked from 'package:R.oo':

    clone

This is rChoiceDialogs 1.0.6 2014-09-05
This is IdMappingAnalysis 1.16.0 2013-05-24
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/IdMappingAnalysis/CorrData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CorrData
> ### Title: CorrData class
> ### Aliases: CorrData
> ### Keywords: classes
> 
> ### ** Examples
> 
>  corrData<-CorrData(examples$uniquePairs,
+ 		examples$msmsExperimentSet,examples$mrnaExperimentSet,verbose=TRUE);
extracting subset by row names...
extracting subset by row names...
extracting subset by column names...
extracting subset by column names...
Creating data structure for correlations...
>  class(corrData);
[1] "CorrData" "Object"  
>  
> 
> 
> 
> 
> dev.off()
null device 
          1 
>