RankingPermutation {GeneSelector} | R Documentation

## Ranking based on permutation tests.

### Description

The function is a wrapper for `mt.sample.teststat` from the package `multtest` (Dudoit et al, 2003). The ranking is here based on permutation p-values first, followed by the absolute value of the statistic. For `S4` method information, see RankingPermutation-methods.

### Usage

    RankingPermutation(x, y, type = "unpaired", B = 100, gene.names = NULL, ...)

### Arguments

`x` | A `matrix` of gene expression values with rows corresponding to genes and columns corresponding to observations or alternatively an object of class `ExpressionSet`.
`y` | If `x` is a matrix, then `y` may be a `numeric` vector or a factor with at most two levels. If `x` is an `ExpressionSet`, then `y` is a character specifying the phenotype variable in the output from `pData`.
`type` | Only the two sample case, `type="unpaired"` is possible.
`B` | The number of permutations to generate. Defaults to 100, but should be increased if computing power admits. Taking `B` too high, however, can lead to long computation time, especially if called from GetRepeatRanking
`gene.names` | An optional vector of gene names.
`...` | Further arguments passed to `mt.sample.teststat` from the package `multtest`. Can be used, for example, to select the statistic to be computed. By default this is `"t.equalvar"` (t-test with equal variances assumed).

### Value

An object of class `GeneRanking`

### Note

The p-values, on which the ranking is primarily based, suffer from the discreteness of the procedure. They follow a step function with jump heights `1/B`.

### Author(s)

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

### References

Dudoit, S., Shaffer, J.P., Boldrick, J.C. (2003).
Multiple Hypothesis Testing in Microarray Experiments Statistical Science, 18, 71-103

### See Also

GetRepeatRanking, RankingTstat, RankingFC, RankingWelchT, RankingWilcoxon, RankingBaldiLong, RankingFoxDimmic, RankingLimma, RankingEbam, RankingWilcEbam, RankingSam, RankingBstat, RankingShrinkageT, RankingSoftthresholdT, RankingGap

### Examples

    ### Load toy gene expression data
    data(toydata)
    ### class labels
    yy <- toydata[1,]
    ### gene expression
    xx <- toydata[-1,]
    ### run RankingPermutation (100 permutations)
    perm <- RankingPermutation(xx, yy, B=100, type="unpaired")

[Package GeneSelector version 1.4.0 Index]