GetStabilityUnion {GeneSelector} | R Documentation

## Stability measures for gene lists

### Description

The similarity of multiple ordered genelists is assessed by counting the size of the union ('union count') for each position in the list. The higher the union count, the less stable are the ordered lists. Similarly to the 'overlap score' of Yang et al. (2006), Lottaz et al. (2006), we compute a weighted average of the union count entitled 'union score' .

### Usage

    GetStabilityUnion(RR, decay = c("linear", "quadratic", "exponential"),
                        alpha = 1, noinformation = 0,...)

### Arguments

`RR` | An object of class `RepeatedRanking`
`decay` | Argument controlling the weight decay of the weights used for the computation of the union 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 union score, not for the union count.
`alpha` | s. `decay`.
`noinformation` | If `noinformation` is a positive integer, union count and -score in the no-information case are approximated by randomly generating multiple lists and computing scores `noinformation` times and averaging the results. Note that this procedure can be rather slow, depending on the number and the length of the lists to be compared.
`...` | Currently unused argument.

### Value

An object of class StabilityOverlap

### Note

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

- Note that this function yields exactly one stability score for multiple lists, as opposed to the pairwise approach in GetStabilityOverlap and GetStabilityDistance.

### Author(s)

Martin Slawski
Anne-Laure Boulesteix

### References

Stolovitzky, G. (2003). Gene selection in microarray data: the elephant, the blind men, and our algorithms. Current Opinion in Structural Biology 13, 370-376.

Jurman, G., Merler, S., Barla, A., Paoli, S., Galea, A., Furlanello, C. (2008).
Algebraic stability indicators for ranked lists in molecular profiling. Bioinformatics 24, 258-264

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_union_ordT <- GetStabilityUnion(loor_ordT, decay="linear")
    ### display the result
    plot(stab_union_ordT)

[Package GeneSelector version 2.30.0 Index]