CombinedRanking-class {GeneSelector} | R Documentation

## "CombinedRanking"

### Description

Object returned from a call to `GeneSelector`.

### Slots

`ranking`:
  'Final' ranking, usually obtained by combinining several statistics. The generation of this ranking is described in GeneSelector.
  The first entry contains the index of the gene ranked highest, as in GeneRanking.
`rankmatrix`:
  Matrix of rankings, arranged in a way that the rankings from the most important statistic is in column 1. In contrast to `ranking`, the first row contains the rankings of the gene with the first index. This slot is used rather for internal reasons.
`inout`:
  Matrix arranged in the same way as `rankmatrix`, but information is now binary: If the specified threshold, then there is a `"+"` symbolizing selection, whereas a `"-"` symbolizes removal.
`selected`:
  The indices of those genes that fall below the specified threshold. Can be accessed more conveniently using `SelectedGenes`
`adjpval`:
  Numeric vector of adjusted p-values, ordered according to `ranking`. `NA` if no adjustment has been taken place (in the case that the threshold was fixed by the user).
`maxrank`:
  Threshold rank, either defined by the user or obtained via p-value adjustment.
`statistics`:
  The names of the statistics used, ordered according to their importance (as defined by the user).
`absdist`:
  Absolute (`L1`) distance from (theoretically) best possible result (rank 1 in all rankings), ordered according to `ranking`. Note that minimum `absdist` does not imply best rank and vice versa, because the computed distance does not weigh different statistics differently.
`reldist`:
  A 'normalized' version of `absdist` (lies in [0;1]).

### Methods

show
  Use `show(object)` for brief information.
toplist
  Use `toplist(object, k=10)` to get information about the top `k=10` genes.
  The ranking used is a synthesis from several statistics.
SelectedGenes
  Use `SelectedGenes(object)` to show all genes that have been selected by the GeneSelector.
GeneInfoScreen
  Use `GeneInfoScreen, which=1` to get detailed information about the gene with index 1, arranged in a pretty plot.
plot
  Use `plot(object)` to visualize relative distances, s. plot,CombinedRanking

### Author(s)

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

[Package GeneSelector version 1.2.0 Index]