RepeatedRanking-class {GeneSelector} | R Documentation

## "RepeatedRanking"

### 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 `NA`s.

`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

[Package GeneSelector version 2.30.0 Index]