GetStabilityOverlap {GeneSelector} | R Documentation |
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.
GetStabilityOverlap(RR, decay = c("linear", "quadratic", "exponential"), scheme = c("rank", "pval"), ...)
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. |
An object of class GetStabilityOverlap
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.
Martin Slawski martin.slawski@campus.lmu.de
Anne-Laure Boulesteix http://www.slcmsr.net/boulesteix
Lottaz, C., Yang, X., Scheid, S., Spang, R. (2006)
OrderedList - a Bioconductor package for detecting
similarity in ordered gene lists.
Bioinformatics, 22, 2315-2316
GetRepeatRanking, GetStabilityLm, RecoveryScore, GetAlpha
## 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 )