StabilityUnion-class: "StabilityUnion"

Description

An object returned from a call to GetStabilityUnion.

Arguments

Slots

union:: A numeric vector of scores derived from union counts, normalized such that 1 is the maximum attainable value. The entries correspond to the positions in the list such that the i-th entry contains the score derived from the union count up to position i.
unionscore:: A numeric vector of union scores, arranged analogously to union.
noinformation:: A list containing an approximation to the expected union count and -score if noinformation in GetStabilityUnion has been set to a positive integer. Otherwise, the list is empty.
decay: The decay scheme used for the weights, s. GetStabilityUnion.

Methods

show: Use show(object) for brief information.
plot: plot(object, frac=1/50, ...) produces a graphical display of the union count (upper panel) and union score (lower panel) for increasing list position, ranging from 1 to frac*number of genes. The ... argument may be used to modify graphical options.

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