RankingSam: Ranking based on the SAM statistic
In GeneSelector: Stability and Aggregation of ranked gene lists

Description Usage Arguments Value Note Author(s) References See Also Examples

A wrapper function to the samr package.

1	RankingSam(x, y, type = c("unpaired", "paired", "onesample"), pvalues = TRUE, 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`	"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.
`pvalues`	Should p-values be computed ? Default is `TRUE`.
`gene.names`	An optional vector of gene names.
`...`	Further arguments to be passed to `samr`. Consult the help of the `samr` package for details.

An object of class GeneRanking.

The computing time is relatively high, due to the fact that permutation statistics are generated.

Martin Slawski
Anne-Laure Boulesteix

Tusher, V.G., Tibshirani, R., and Chu, G. (2001).
Significance analysis of microarrays applied to the ionizing radiation response. PNAS, 98, 5116-5121.

Schwender, H., Krause, A. and Ickstadt, K. (2003).
Comparison of the Empirical Bayes and the Significance Analysis of Microarrays. Technical Report, University of Dortmund.

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

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