R: plotErrorsFoldTwoLayerCV Method to plot the error rate of a...
plotErrorsFoldTwoLayerCV-methods
R Documentation
plotErrorsFoldTwoLayerCV Method to plot the error rate of a two-layer Cross-validation
Description
This method creates a plot that reprenset the error rate in each fold of each repeat of the
second layer of cross-validation of the two-layer cross-validation of the assessment at stake. The plot
represents the error rate 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.
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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> 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/plotErrorsFoldTwoLayerCV-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotErrorsFoldTwoLayerCV-methods
> ### Title: plotErrorsFoldTwoLayerCV Method to plot the error rate of a
> ### two-layer Cross-validation
> ### Aliases: plotErrorsFoldTwoLayerCV plotErrorsFoldTwoLayerCV-methods
> ### plotErrorsFoldTwoLayerCV,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 <- runTwoLayerExtCV(expeOfInterest)
>
> plotErrorsFoldTwoLayerCV(expeOfInterest)
>
>
>
>
>
>
> dev.off()
null device
1
>