RankingGap {GeneSelector} | R Documentation |
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.
RankingGap(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.
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.
Martin Slawski martin.slawski@campus.lmu.de
Anne-Laure Boulesteix http://www.slcmsr.net/boulesteix
GetRepeatRanking, RankingTstat, RankingFC, RankingWelchT, RankingWilcoxon, RankingBaldiLong, RankingFoxDimmic, RankingLimma, RankingEbam, RankingWilcEbam, RankingSam, RankingBstat, RankingShrinkageT, RankingSoftthresholdT, RankingPermutation
## 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")