plotErrorsRepeatedOneLayerCV Method to plot the estimated error rates in each repeat of a one-layer Cross-validation

Description

This method creates a plot that represent the summary estimated error rate and the cross-validated error rate in each repeat of the one-layer cross-validation of the assessment at stake. The plot represents the summary estimate of the error rate (averaged over the repeats) and the cross-validated error rate obtained in each repeat versus the size of gene subsets (for SVM-RFE) or the threshold values (for NSC).

Methods

object = "assessment"

The method is only applicable on objects of class assessment.

See Also

plotErrorsFoldTwoLayerCV-methods, plotErrorsSummaryOneLayerCV-methods

Examples

data('vV70genesDataset')

expeOfInterest <- new("assessment", dataset=vV70genes,
                                   noFolds1stLayer=3,
                                   noFolds2ndLayer=2,
                                   classifierName="svm",
                                   typeFoldCreation="original",
                                   svmKernel="linear",
                                   noOfRepeat=10,
                                   featureSelectionOptions=new("geneSubsets", optionValues=c(1,2,3,4,5,6)))

expeOfInterest <- runOneLayerExtCV(expeOfInterest)

plotErrorsRepeatedOneLayerCV(expeOfInterest)

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(Rmagpie)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Rmagpie/plotErrorsRepeatedOneLayerCV.rd_%03d_medium.png", width=480, height=480)
> ### Name: plotErrorsRepeatedOneLayerCV-methods
> ### Title: plotErrorsRepeatedOneLayerCV Method to plot the estimated error
> ###   rates in each repeat of a one-layer Cross-validation
> ### Aliases: plotErrorsRepeatedOneLayerCV
> ###   plotErrorsRepeatedOneLayerCV-methods
> ###   plotErrorsRepeatedOneLayerCV,assessment-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> data('vV70genesDataset')
> 
> expeOfInterest <- new("assessment", dataset=vV70genes,
+                                    noFolds1stLayer=3,
+                                    noFolds2ndLayer=2,
+                                    classifierName="svm",
+                                    typeFoldCreation="original",
+                                    svmKernel="linear",
+                                    noOfRepeat=10,
+                                    featureSelectionOptions=new("geneSubsets", optionValues=c(1,2,3,4,5,6)))
> 
> expeOfInterest <- runOneLayerExtCV(expeOfInterest)
> 
> plotErrorsRepeatedOneLayerCV(expeOfInterest)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>