GeneRanking-class {GeneSelector} | R Documentation

## "GeneRanking"

### Description

Object returned by all implemented Ranking methods (RankingTstat,RankingFC, RankingWelchT, RankingWilcoxon, RankingBaldiLong, RankingFoxDimmic, RankingLimma, RankingEbam, RankingWilcEbam, RankingSam, RankingBstat, RankingShrinkageT, RankingSoftthresholdT, RankingPermutation, RankingGap)

### Slots

`x`:
  A `matrix` storing gene expression, rows correspond to genes, columns to samples (arrays).
`y`:
  A `factor` with two levels of class labels.
`statistic`:
  A `numeric` vector storing the statistics, ordered according to the `ranking`.
`ranking`:
  A vector of indices that represents the ranking of the genes. The first entry corresponds to the best one. The ranking is determined via the statistic (size of absolute value), so there is no distinction of over- and underexpression. For example, if there are five genes with indices `1,2,3,4,5`, `ranking=3,4,2,1,5` means that the gene with index 3 is ranked highest, having the largest statisitic (in absolze value), gene 4 has rank 2, and so on.
`pval`:
  The ordered vector of p-values.
  `NA` if pvalues have not been computed.
`type`:
  Type of the test (one of "`unpaired`", "`paired`", "`onesample`").
`method`:
  Short name of the ranking Method.

### Methods

show
  Use `show(GeneRanking-object)` for brief information.
summary,GeneRanking
  Use `summary(GeneRanking-object)` For a five-point-summary of statistics and p-values.
toplist
  Use `toplist(object, k=10)` to get information about the top `k=10` genes.

### Author(s)

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

### See Also

RepeatRanking, GetRepeatRanking

[Package GeneSelector version 1.2.0 Index]