GetStabilityOverlap {GeneSelector}R Documentation

Stability measures for gene rankings

Description

The similarity of two ordered genelists is assessed by a 'weighted cumulative sum' of the number of overlaps up to a certain position in the list and is called 'Overlap Score'. For further information, consult the reference given below.

Usage

GetStabilityOverlap(RR, decay = c("linear", "quadratic", "exponential"), 
                    scheme = c("rank", "pval"), ...)

Arguments

RR An object of class RepeatRanking
scheme Whether ranks ((scheme="rank")) or p-values ((scheme="pval")) should be used as basis of weighting.
decay argument controlling the weight decay for the weights used in the overlap score. If decay=linear, then we have weight 1/s for rank/p-value s, if decay=quadratic, then the weight is 1/s^2 and if decay=quadratic, then the weight is exp(-s*alpha) where alpha is a tuning parameter, specified via the argument alpha
... Currently unused argument.

Value

An object of class GetStabilityOverlap

Note

The computed overlap differs from the version described above in one point: Here, the overlap score are normalized to fall into the unit interval for better interpretability.

Author(s)

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

References

Lottaz, C., Yang, X., Scheid, S., Spang, R. (2006)
OrderedList - a Bioconductor package for detecting similarity in ordered gene lists. Bioinformatics, 22, 2315-2316

See Also

GetRepeatRanking, GetStabilityLm, RecoveryScore, GetAlpha

Examples

 ## Load toy gene expression data
data(toydata)
### class labels
yy <- toydata[1,]
### gene expression
xx <- toydata[-1,]
### get ranking 
ordT <- RankingTstat(xx, yy, type="unpaired")
### Generate Leave-One-Out
loo <- GenerateFoldMatrix(xx, yy, k=1)
### Repeat Ranking with t-statistic
loor_ordT <- GetRepeatRanking(ordT, loo)
### assess stability
stab_ov_ordT <- GetStabilityOverlap(loor_ordT, decay="linear")
### for a short summary
summary(stab_ov_ordT)
### for a graphical display
plot(stab_ov_ordT )

[Package GeneSelector version 1.4.0 Index]