ResubstituteParams-class: Parameters for Resubstitution Error Calculation

In ClassifyR: A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing

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 10, 20, 30, 40, 50, 60, 70, 80, 90, 100. 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 rate for.

performanceType

One of the eleven types of performance metrics which can be calculated by calcCVperformance.

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 the classifier.

...

Other named parameters which will be used by the classifier.

Author(s)

Dario Strbenac

Examples

  ResubstituteParams(nFeatures = seq(25, 1000, 25), performanceType = "error", better = "lower")

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

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
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] "error"

Slot "better":
[1] "lower"

Slot "otherParams":
list()

ClassifyR documentation built on Nov. 8, 2020, 6:53 p.m.