AggregatePenalty: Aggregation of repeated rankings using a variance penalty...

In GeneSelector: Stability and Aggregation of ranked gene lists

Description

The idea behind this form of aggregation is to find a compromise between quality on the one hand, represented by the list position/rank, and variability on the other hand. The latter is assessed by calling the function dispersion.

Usage

AggregatePenalty(RR, dispersion = c("sd", "mad", "iqr"), center = NULL, gamma = 0.05,...)

Arguments

RR	An object of class RepeatedRanking.
dispersion	The dispersion measure to be used (s. dispersion): "sd" standard deviation, "mad" median absolute deviation, "iqr" interquartile range.
center	Optional numeric vector specifying for each gene the rank serving as center/location parameter for dispersion. If center = NULL, the reference ranking RR@original@ranking is used.
gamma	As basis of the aggregated ranking, the quantity (1-gamma)*center + gamma * dispersion is used, i.e. the variability aspect dominates as gamma tends to one.
...	Further arguments passed to dispersion.

Value

An object of class AggregatedRanking.

Author(s)

Martin Slawski
Anne-Laure Boulesteix

See Also

RepeatRanking, AggregateSimple, AggregateSVD, AggregateMC

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(y = yy, k=1)
### Get all rankings
loor_ordT <- RepeatRanking(ordT, loo)
### aggregate rankings
agg_pen_ordT <- AggregatePenalty(loor_ordT, dispersion = "iqr", gamma = 0.3)
toplist(agg_pen_ordT)

GeneSelector documentation built on May 1, 2019, 11:35 p.m.