The Bootstrap class

Description

Package: IdMappingAnalysis
Class Bootstrap

Object
~~|
~~+--IdMapBase
~~~~~~~|
~~~~~~~+--Bootstrap

Directly known subclasses:

public static class Bootstrap
extends IdMapBase

The Bootstrap object encapsulates a data frame containing the unique pairs in the first two columns and the correlation results, sd and bias obtained from the bootstrapping procedure in the next 3 columns During the object creation, the bootstrapping procedure is applyied to each row of the experiment set pairs from the CorrData object optionally applying the Fisher transform to the correlation data.

Usage

Bootstrap(corrData=NULL, Fisher=FALSE, R=200, verbose=FALSE, ...)

Arguments

Value

A Bootstrap object encapsulating the data.frame with following columns:

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

 bootstrap<-Bootstrap(examples$corrData,R=20,verbose=TRUE);
 class(bootstrap);
 bootstrap[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/Bootstrap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Bootstrap
> ### Title: The Bootstrap class
> ### Aliases: Bootstrap
> ### Keywords: classes
> 
> ### ** Examples
> 
>  bootstrap<-Bootstrap(examples$corrData,R=20,verbose=TRUE);
Performing bootstrap R= 20 on correlations...
                                                       processed: 1 %                                                        processed: 2 %                                                        processed: 3 %                                                        processed: 4 %                                                        processed: 5 %                                                        processed: 6 %                                                        processed: 7 %                                                        processed: 8 %                                                        processed: 9 %                                                        processed: 10 %                                                        processed: 11 %                                                        processed: 12 %                                                        processed: 13 %                                                        processed: 14 %                                                        processed: 15 %                                                        processed: 16 %                                                        processed: 17 %                                                        processed: 18 %                                                        processed: 18 %                                                        processed: 19 %                                                        processed: 20 %                                                        processed: 21 %                                                        processed: 22 %                                                        processed: 23 %                                                        processed: 24 %                                                        processed: 25 %                                                        processed: 26 %                                                        processed: 27 %                                                        processed: 28 %                                                        processed: 29 %                                                        processed: 30 %                                                        processed: 31 %                                                        processed: 32 %                                                        processed: 33 %                                                        processed: 34 %                                                        processed: 35 %                                                        processed: 36 %                                                        processed: 37 %                                                        processed: 38 %                                                        processed: 39 %                                                        processed: 40 %                                                        processed: 41 %                                                        processed: 42 %                                                        processed: 43 %                                                        processed: 44 %                                                        processed: 45 %                                                        processed: 46 %                                                        processed: 47 %                                                        processed: 48 %                                                        processed: 49 %                                                        processed: 50 %                                                        processed: 51 %                                                        processed: 52 %                                                        processed: 53 %                                                        processed: 54 %                                                        processed: 55 %                                                        processed: 55 %                                                        processed: 56 %                                                        processed: 57 %                                                        processed: 58 %                                                        processed: 59 %                                                        processed: 60 %                                                        processed: 61 %                                                        processed: 62 %                                                        processed: 63 %                                                        processed: 64 %                                                        processed: 65 %                                                        processed: 66 %                                                        processed: 67 %                                                        processed: 68 %                                                        processed: 69 %                                                        processed: 70 %                                                        processed: 71 %                                                        processed: 72 %                                                        processed: 73 %                                                        processed: 74 %                                                        processed: 75 %                                                        processed: 76 %                                                        processed: 77 %                                                        processed: 78 %                                                        processed: 79 %                                                        processed: 80 %                                                        processed: 81 %                                                        processed: 82 %                                                        processed: 83 %                                                        processed: 84 %                                                        processed: 85 %                                                        processed: 86 %                                                        processed: 87 %                                                        processed: 88 %                                                        processed: 89 %                                                        processed: 90 %                                                        processed: 91 %                                                        processed: 91 %                                                        processed: 92 %                                                        processed: 93 %                                                        processed: 94 %                                                        processed: 95 %                                                        processed: 96 %                                                        processed: 97 %                                                        processed: 98 %                                                        processed: 99 % 
>  class(bootstrap);
[1] "Bootstrap" "IdMapBase" "Object"   
>  bootstrap[1:10,];
   Uniprot         Affy        corr         sd          bias
1   P04264    205900_at -0.01757533 0.13552788 -0.0966990939
2   P13645  207023_x_at -0.03609131 0.06605149 -0.0083416703
3   P13645  210633_x_at -0.09975384 0.06109327  0.0054310240
4   P13645  213287_s_at -0.06143428 0.07177885 -0.0106051890
5   P35908    207908_at -0.08162018 0.08697563 -0.0002873034
6   P08729  209016_s_at  0.56948664 0.04530826 -0.0208437248
7   P08729  214031_s_at  0.41598893 0.05202768 -0.0269534942
8   P08729 1558394_s_at -0.19035282 0.07879690  0.0116187101
9   P08729   1558393_at  0.32316744 0.10070811 -0.0088709677
10  P08727    201650_at  0.42170144 0.04988358  0.0155985976
>  
> 
> 
> 
> 
> dev.off()
null device 
          1 
>