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 1.2.0 Index]