StabilityOverlap-class {GeneSelector} | R Documentation

## "StabilityOverlap"

### Description

An object returned from a call to GetStabilityOverlap.

### Slots

`intersection`:

  A matrix of intersection counts, normalized such that 1 is the maximum attainable value. The rows correspond to the positions in the list such that row `i` contains the number of common elements of two lists up to position `i`. The columns correspond to lists, either obtained from altered datasets or by applying multiple ranking procedures.

`overlapscore`:

  A matrix of overlap scores, arranged analogously to `intersection`.

`noinformation`:

  A list containing two numeric vectors named `"intersection"` and `"overlap score"` containing for each list position intersection counts and overlap scores one would expect in the no-information case, corresponding to the random generation of two mutually independent lists.

`scheme`

  s. GetStabilityOverlap.

`decay`

  The decay scheme used for the weights, s. GetStabilityOverlap.

### Methods

show

  Use `show(object)` for brief information.

summary

  Use `summary(object), measure = c("overlapscore", "intersection"), display = c("summary", "all"), position, digits = 3` for condensed output. The argument `measure` specifies the measure one is interested in. The argument `display` controls whether only a five-point summary is printed (`display = "summary"`) or whether all results are printed (`display = "all"`). The argument `position` specifies the list position, e.g. if `position = 10`, then intersection counts/overlap scores up to position 10 are summarized. The argument `digits` is used for number formatting. Note that the output depends on `scheme`.

plot

  `plot(object, frac=1/50, mode = c("mean", "all", "specific"), which = 1, ...)` produces a graphical display of the intersection count (upper panel) and the overlap score (lower panel) for increasing list position, ranging from `1` to `frac*number of genes`. The argument mode specifies whether this is done as average over all lists (`mode = "mean"`), for a certain alternative list `which` (`mode = "specific"`) or succesively in the form of separate plots for each alternative list (`mode = "all"`). The `...` argument may be used to modify graphical options.

### 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

[Package GeneSelector version 2.30.0 Index]