The Corr class

Description

Package: IdMappingAnalysis
Class Corr

Object
~~|
~~+--IdMapBase
~~~~~~~|
~~~~~~~+--Corr

Directly known subclasses:

public static class Corr
extends IdMapBase

Create the Corr object by performing correlations on the CorrData object using the correlation algorithm defined by the method argument. The Corr object encapsulates a data.frame containing three columns: the first two are unique pairs and the third is a correlation results with a column name reflecting the correlation method ('pearson', 'spearman' or 'kendall').

Usage

Corr(corrData=NULL, method="pearson", verbose=FALSE, ...)

Arguments

Fields and Methods

Methods:

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

 corr<-Corr(examples$corrData,method="spearman",verbose=TRUE);
 class(corr);
 corr[1:10,];
 

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/Corr.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Corr
> ### Title: The Corr class
> ### Aliases: Corr
> ### Keywords: classes
> 
> ### ** Examples
> 
>  corr<-Corr(examples$corrData,method="spearman",verbose=TRUE);
Performing correlations...
>  class(corr);
[1] "Corr"      "IdMapBase" "Object"   
>  corr[1:10,];
   Uniprot         Affy     spearman
1   P04264    205900_at  0.024291216
2   P13645  207023_x_at -0.027788785
3   P13645  210633_x_at -0.003908609
4   P13645  213287_s_at  0.018822357
5   P35908    207908_at -0.169953880
6   P08729  209016_s_at  0.754577016
7   P08729  214031_s_at  0.400838395
8   P08729 1558394_s_at -0.134991491
9   P08729   1558393_at  0.279826545
10  P08727    201650_at  0.591236511
>  
> 
> 
> 
> 
> dev.off()
null device 
          1 
>