RankingWelchT {GeneSelector}R Documentation

Ranking based on the Welch t statistic.

Description

Performs univariate (rowwise) Welch tests on a gene expression matrix. The Welch t statistic is a better alternative to the 'ordinary' t statistic in the two sample, unequal variances setting.

Usage

RankingWelchT(x, y, type = "unpaired", pvalues = TRUE, 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. Otherwise, use RankingTstat. Variances are assumed to be unequal.

pvalues

Should p-values be computed ? Default is TRUE.

gene.names

An optional vector of gene names.

...

Currenly unused argument.

Value

An object of class GeneRanking.

Author(s)

Martin Slawski
Anne-Laure Boulesteix

See Also

RepeatRanking, RankingTstat, RankingFC, RankingWilcoxon, 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 RankingWelch
welchT <- RankingWelchT(xx, yy, type="unpaired")

[Package GeneSelector version 2.30.0 Index]