RepeatRanking-class {GeneSelector} | R Documentation

## "RepeatRanking"

### Description

Object returned by a call to GetRepeatRanking

### Slots

`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 `NA`s.
`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.

### Methods

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

### Author(s)

Martin Slawski martin.slawski@campus.lmu.de
Anne-Laure Boulesteix http://www.slcmsr.net/boulesteix

### See Also

GeneRanking, GetRepeatRanking

[Package GeneSelector version 1.4.0 Index]