RepeatedRanking-class: "RepeatedRanking"

Description Slots Methods Author(s) See Also

Description

Object returned by a call to RepeatRanking or MergeMethods

Slots

original:

The ranking based on the original data set (output from RepeatRanking) or on a reference method (output from MergeMethods), represented by an object of class GeneRanking

rankings:

The rankings obtained from altered datasets (output from RepeatRanking or from different methods (output from MergeMethods), stored as a matrix. One column represents one replication (output from RepeatRanking or one method (output from MergeMethods). Each column is of the same structure as the slot ranking of the class GeneRanking.

pvals:

The matrix of p-values stored analogously to rankings. If p-values have not been computed, this is a matrix of NAs.

statistics:

The statistics obtained from altered data sets, stored analogously to rankings

scheme:

A character for the resampling scheme, can be one of "subsampling", "labelexchange", "bootstrap", "jittering" (if noise has been added), "merged (rankings)" if several resampling schemes for the same dataset and ranking method have been combined via the MergeRankings-method, or "merged (methods)" if the rankings of several methods have been combined via the MergeMethods-method.

Methods

show

Use show(RepeatedRanking-Object) for brief information.

toplist

Use toplist(RepeatedRanking-Object, k=10) to get information about the top k=10 genes for each ranking and one overview table showing frequencies of gene indices for each of the ranks 1,...k. Additionally, only the overview table can be shown with all other output suppressed using toplist(RepeatedRanking-Object, show=FALSE).

dispersion

Genewise variance estimation, s. dispersion,RepeatedRanking-method

MergeRankings

Use MergeRankings(RepeatedRanking-Object1, RepeatedRanking-Object2) to combine results from different resampling schemes. The results is again an object of class RepeatedRanking where the slot scheme is "merged (rankings)" and all matrices have been concatenated columnwise.

plot

Use plot(RepeatedRanking-Object) for a scatterplot of the reference ranking (slot original) vs. alternative rankings (slot rankings).

HeatmapRankings

s. HeatmapRankings

Author(s)

Martin Slawski
Anne-Laure Boulesteix

See Also

GeneRanking, RepeatRanking, MergeMethods, dispersion, HeatmapRankings


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