Results from the feature selection method

Description

Results from the feature selection method.

Usage

data(stabilitySelection)

Format

The format is: List of 4 $ selected : chr [1:25] "count" "cell.act.m.majoraxis" "nuc.nuc.b.q001" "nuc.0.m.eccentricity" ... $ correlation : num [1:25] 0.917 0.972 0.938 0.928 0.896 ... $ ratioPositive : num [1:25] 1 1 0.947 0.942 0.937 ... $ correlationAll: List of 25 ..$ : Named num [1:227] 0.917 0.884 0.93 0.897 0.882 ... .. ..- attr(*, "names")= chr [1:227] "count" "nuc.0.m.majoraxis" "nuc.0.m.eccentricity" "nuc.0.s.area" ... ..$ : Named num [1:226] 0.884 0.931 0.899 0.887 0.9 ... .. ..- attr(*, "names")= chr [1:226] "nuc.0.m.majoraxis" "nuc.0.m.eccentricity" "nuc.0.s.area" "nuc.0.s.perimeter" ... ..$ : Named num [1:225] 0.884 0.934 0.884 0.882 0.883 ... .. ..- attr(*, "names")= chr [1:225] "nuc.0.m.majoraxis" "nuc.0.m.eccentricity" "nuc.0.s.area" "nuc.0.s.perimeter" ... ...

Details

selected is a vector of the selected feature namess. correlation are the Pearson correlation coefficients of the residual features. ratioPositive is the fraction of positively correlated features among all candidate features for selection. correlationAll contains a vector of correlations of the residual features of all candidate features for each step in the selection process.

References

Laufer, Fischer et al., 2013

See Also

HD2013SGI

Examples

data(stabilitySelection, package="HD2013SGI")
barplot(stabilitySelection$correlation,
        names.arg=stabilitySelection$selected,las=2)
barplot(stabilitySelection$ratioPositive-0.5, offset=0.5,
        names.arg=stabilitySelection$selected,las=2)

Results

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> library(HD2013SGI)
Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: geneplotter
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: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:gplots':

    space

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    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML
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Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:geneplotter':

    plotMA

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: vcd
Loading required package: grid

Attaching package: 'vcd'

The following object is masked from 'package:IRanges':

    tile

Loading required package: LSD
Loading required package: EBImage

Attaching package: 'EBImage'

The following object is masked from 'package:vcd':

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

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> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/HD2013SGI/stabilitySelection.Rd_%03d_medium.png", width=480, height=480)
> ### Name: stabilitySelection
> ### Title: Results from the feature selection method
> ### Aliases: stabilitySelection
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(stabilitySelection, package="HD2013SGI")
> barplot(stabilitySelection$correlation,
+         names.arg=stabilitySelection$selected,las=2)
> barplot(stabilitySelection$ratioPositive-0.5, offset=0.5,
+         names.arg=stabilitySelection$selected,las=2)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>