StabilityOverlap-class: "StabilityOverlap"

In GeneSelector: Stability and Aggregation of ranked gene lists

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

GeneSelector documentation built on May 1, 2019, 11:35 p.m.