GeneSelector (version 2.22.0)

RankingWilcoxon: Ranking based on the Wilcoxon statistic

Description

The Wilcoxon statistic is rank-based and 'distribution free'. It is equivalent to the Mann-Whitney statistic and also related to the 'area under the curve' (AUC) in the two sample case. The implementation is efficient, but still far slower than that of the t-statistic.

Usage

RankingWilcoxon(x, y, type = c("unpaired", "paired", "onesample"), pvalues = FALSE, 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, Wilcoxon Rank Sum test is performed.

"paired":

Wilcoxon sign rank test is performed on the differences.

"onesample":

y has only one level. The Wilcxon sign rank test for difference from zero is performed.

pvalues

Should p-values be computed ? Default is FALSE.

gene.names

An optional vector of gene names.

...

Currently unused argument.

Value

GeneRanking.

See Also

RepeatRanking, RankingTstat, RankingFC, RankingWelchT, RankingBaldiLong, RankingFoxDimmic, RankingLimma, RankingEbam, RankingWilcEbam, RankingSam, RankingShrinkageT, RankingSoftthresholdT, RankingPermutation

Examples

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