RankingGap {GeneSelector} | R Documentation

## Ranking based on 'gaps'

### Description

The ranking is based on the gap between two classes (for `type="unpaired"`) where the gap is defined as `gap(1,2) = max(min2 - max1, min1-max2, 0)`, where min1, max1 are the minimum/maximum observed values from class 1 (analogously for min2, max2). It is only greater than zero if classes do not overlap. For `type="paired", "onesample"` the gap, i.e. absolute distance from the origin is computed.
For `S4` method information, see RankingFC-methods.

### Usage

    RankingGap(x, y, type = c("unpaired", "paired", "onesample"), 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`. If `type = paired`, the first half of the columns corresponds to the first measurements and the second half to the second ones. For instance, if there are 10 observations, each measured twice, stored in an expression matrix `expr`, then `expr[,1]` is paired with `expr[,11]`, `expr[,2]` with `expr[,12]`, and so on.
`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`. If `type = paired`, take care that the coding is analogously to the requirement concerning `x`
`type` | "unpaired": two-sample test. "paired": paired test. Take care that the coding of `y` is correct (s. above) "onesample": `y` has only one level. Test whether the true mean is different from zero.
`gene.names` | An optional vector of gene names.
`...` | Currently unused argument.

### Value

An object of class GeneRanking.

### Note

In most cases, classes will not be separated by only one gene. Consequently, the great majority of statistics will be zero.
p-values are not available.

### Author(s)

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

### See Also

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

### Examples

    ## Load toy gene expression data
    data(toydata)
    ### class labels
    yy <- toydata[1,]
    ### gene expression
    xx <- toydata[-1,]
    ### run RankingGap
    gapstat <- RankingGap(xx, yy, type="unpaired")

[Package GeneSelector version 1.2.0 Index]