GetStabilityOverlap: 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

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

StabilityOverlap

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

Examples

Run this code

 ## 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)