RankingShrinkageT {GeneSelector} | R Documentation |
The shrinkage t statistic stabilizes the estimated variances
appearing in the denominator of the statistic via a
James-Stein-Shrinkage approach (Opgen-Rhein and Strimmer,2007). In this implementation,
the shrinkage target is the median of the variances.
For S4
method information, see RankingShrinkageT-methods.
RankingShrinkageT(x, y, type = c("unpaired", "paired", "onesample"), gene.names = NULL, ...)
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 |
|
gene.names |
An optional vector of gene names. |
... |
Currently unused argument. |
An object of class GeneRanking.
Martin Slawski martin.slawski@campus.lmu.de
Anne-Laure Boulesteix http://www.slcmsr.net/boulesteix
Opgen-Rhein, R., Strimmer, K. (2007).
Accurate Ranking of Differentially Expressed Genes
by a Distribution-Free Shrinkage Approach.
Statistical Applications in Genetics and
Molecular Biology, Vol. 6, Iss. 1, Art.9
GetRepeatRanking, RankingTstat, RankingFC, RankingWelchT, RankingWilcoxon, RankingBaldiLong, RankingFoxDimmic, RankingLimma, RankingEbam, RankingWilcEbam, RankingSam, RankingBstat, RankingSoftthresholdT, RankingPermutation, RankingGap
### Load toy gene expression data data(toydata) ### class labels yy <- toydata[1,] ### gene expression xx <- toydata[-1,] ### run RankingShrinkageT shrinkaget <- RankingShrinkageT(xx, yy, type="unpaired")