GetStabilityOverlap {GeneSelector} | R Documentation

## Stability measures for gene lists

### Description

The similarity of two ordered genelists is assessed by counting the size of the intersection ('overlap') for each position in the list and by computing a weighted cumulative sum of the number of overlaps up to a position in the list ('overlap score'), as suggested by Yang et al. (2006) and Lottaz et al. (2006).

### Usage

    GetStabilityOverlap(RR, scheme = c("original", "pairwise"), decay = c("linear", "quadratic", "exponential"),
                        alpha = 1, ...)

### Arguments

`RR` | An object of class `RepeatedRanking`
`scheme` | If `scheme = "original"`, a reference list is compared with alternative lists. If `scheme = "pairwise"`, all possible pairs of lists are compared. The latter is normally used in the absence of a reference list, e.g. if the agreement of different ranking procedures is of interest.
`decay` | Argument controlling the weight decay of the weights necessary for the computation of the overlap score. If `decay="linear"`, then we have weight `1/l` for list position `l`, if `decay="quadratic"`, then the weight is `1/l^2` and if `decay="exponential"`, then the weight is `exp(-alpha*l)` where `alpha` is a tuning parameter, specified via the argument `alpha`. Weights are used only for the overlap score, not for the intersection count.
`alpha` | s. `decay`.
`...` | Currently unused argument.

### Value

An object of class StabilityOverlap

### Note

- Contrary to Yang et al. (2006), Lottaz et al. (2006), we consider differential expression without distinguishing between over- and underexpression.

- Both intersection count and overlap score are suitably normalized to fall into the unit interval for the sake of better interpretability, with zero corresponding to maximal instability.

### Author(s)

Martin Slawski
Anne-Laure Boulesteix

### References

Qiu, X., Xiao, Y., Gordon, A., Yakovlev, A. (2006)
Assessing stability of gene selection in microarray data analysis. BMC Bioinformatics 7, 50

Yang, X., Bentink, S., Scheid, S., Spang, R. (2006)
Similarities of ordered gene lists. Journal of Bioinformatics and Computational Biology 4, 693-708

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

RepeatRanking

### 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(y = yy, k=1)
    ### Repeat Ranking with t-statistic
    loor_ordT <- RepeatRanking(ordT, loo)
    ### assess stability
    stab_ov_ordT <- GetStabilityOverlap(loor_ordT, scheme = "original", decay="linear")
    ### for a short summary
    summary(stab_ov_ordT, measure = "intersection", display = "all", position = 10)
    ### for a graphical display
    plot(stab_ov_ordT)

[Package GeneSelector version 2.30.0 Index]