R: "RepeatRanking"

RepeatRanking-class {GeneSelector}

R Documentation

"RepeatRanking"

Object returned by a call to GetRepeatRanking

original:: The ranking based on the original data set, represented by an object of class "GeneRanking"
rankings:: The rankings obtained from altered datasets, stored as a matrix. One column represents one replication. Each column is arranged in the same manner as the slot ranking of the class GeneRanking, i.e. the first entry of a column contains the index of the gene ranked highest.
pvals:: The p-values obtained from altered data sets, stored analogoulsy to rankings. If p-values have not been computed, this is a matrix of NAs.
statistics:: The statistics obtained from altered data sets, stored analogoulsy to rankings
scheme:: A character for the resampling scheme, can be one of "Subsampling", "Labelexchange", "Bootstrap", "Jittering" (if noise has been added) or "combined" if several resampling schemes for the same dataset and ranking method have been combined via the join-method, s. below.

show: use show(RepeatRanking-Object) for brief information.
toplist: Use toplist(RepeatRanking-Object, k=10) to get information about the top k=10 genes for each replication (=perturbed dataset) and one overall table showing frequencies of gene indices for each of the ranks 1,...k. Additionally, only the overall table can be shown with all other output suppressed using toplist(RepeatRanking-Object, show=FALSE)
variance: Genewise variance estimation, s. variance,RepeatRanking-method
join: use join(RepeatRanking-Object1, RepeatRanking-Object2) to combine results from different resampling schemes. The results is again an object of class RepeatRanking where the slot scheme is "combined" and all matrices have been concatenated columnwise.
plot: use plot(RepeatRanking-Object) for a scatterplot of original rankings and rankings of the perturbed datasets, s. plot,RepeatRanking