R: Parameters for Resubstitution Error Calculation
ResubstituteParams
R Documentation
Parameters for Resubstitution Error Calculation
Description
Some feature selection functions provided in the framework use resubstitution error
rate to choose the best number of features for classification. This class stores
parameters related to that process
Constructor
ResubstituteParams()
Creates a default ResubstituteParams object. The number of features tried is
100, 200, 300, 400, 500. The performance measure used is the balanced error rate.
ResubstituteParams(nFeatures, performanceType, better = c("lower", "higher"))
Creates a ResubstituteParams object, storing information about the number of top
features to calculate the performance measure for, the performance measure to use,
and if higher or lower values of the measure are better.
nFeatures
A vector for the top number of features to test the
resubstitution error for.
performanceType
Either "balanced" or one of the options provided
by performance.
better
Either "lower" or "higher". Determines whether higher
or lower values of the performance measure are desirable.
intermediate
Character vector. Names of any variables created in prior stages by
runTest that need to be passed to classifier.
...
Other named parameters which will be used by the classifier.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
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> library(ClassifyR)
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")'.
Loading required package: BiocParallel
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ClassifyR/ResubstituteParams-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ResubstituteParams
> ### Title: Parameters for Resubstitution Error Calculation
> ### Aliases: ResubstituteParams ResubstituteParams-class
> ### ResubstituteParams,ANY,ANY,ANY-method
> ### ResubstituteParams,numeric,character,character-method
>
> ### ** Examples
>
> ResubstituteParams(nFeatures = seq(25, 1000, 25), performanceType = "err", better = "lower")
An object of class "ResubstituteParams"
Slot "nFeatures":
[1] 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375
[16] 400 425 450 475 500 525 550 575 600 625 650 675 700 725 750
[31] 775 800 825 850 875 900 925 950 975 1000
Slot "performanceType":
[1] "err"
Slot "better":
[1] "lower"
Slot "otherParams":
list()
>
>
>
>
>
> dev.off()
null device
1
>