AggregateSimple {GeneSelector} | R Documentation

## Simple aggregation of repeated rankings

### Description

All rankings obtained from perturbed datasets plus the ranking from the original dataset are aggregated via `aggregatefun`.

### Usage

    AggregateSimple(RR, S, aggregatefun = c("mode", "mean",
                     "median", "quantile"), q = NULL)

### Arguments

`RR` | An object of class `RepeatRanking`.
`S` | Either an object of class `StabilityLm` or `StabilityOverlap`.
`aggregatefun` | The statistic to return as aggregation. mode The rank occuring most frequently. If two or more ranks occur equally often, then weights are used (s.details) mean A weighted mean is used. For information on weights, s.details. median The median of all observed ranks is used. quantile The `q`-quantile of all observed ranks is used.
`q` | Only specified if `aggregatefun=quantile`

### Details

The weights used if `aggregatefun=mode` or `aggregatefun=mean` decrease linear with decreasing similarity of perturbed dataset and original dataset as measured by Stability Measures (object `S`).

### Value

An object of class AggregatedRanking.

### Author(s)

Martin Slawski martin.slawski@campus.lmu.de
Anne-Laure Boulesteix http://www.slcmsr.net/boulesteix

### See Also

GetRepeatRanking, GetStabilityLm, GetStabilityOverlap, AggregateBayes

### Examples

    ## Load toy gene expression data
    data(toydata)
    ### class labels
    yy <- toydata[1,]
    ### gene expression
    xx <- toydata[-1,]
    ### run RankingTstat
    ordT <- RankingTstat(xx, yy, type="unpaired")
    ### Generate Leave-one-out Foldmatrix
    loo <- GenerateFoldMatrix(xx, yy, k=1)
    ### Get all rankings
    loor_ordT <- GetRepeatRanking(ordT, loo)
    ### compute stability measure
    stab_overlap <- GetStabilityOverlap(loor_ordT, decay="linear")
    ### aggregate rankings
    agg_simple_ordT <- AggregateSimple(loor_ordT, stab_overlap, aggregatefun="mean")

[Package GeneSelector version 1.2.0 Index]