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 1.4.0 Index]