RankingFC {GeneSelector} | R Documentation |
Naive ranking that only considers difference in means
without taking variances into account.
For S4
method information, see RankingFC-methods.
RankingFC(x, y, type = c("unpaired", "paired", "onesample"), pvalues = TRUE, gene.names = NULL, LOG = FALSE, ...)
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 |
|
pvalues |
Should p-values be computed ? Defaults to TRUE . |
gene.names |
An optional vector of gene names. |
LOG |
By default, the data are assumed to be already logarithm-ed.
If not, this can be done by setting LOG=TRUE |
... |
Currently unused argument. |
An object of class GeneRanking
Take care that the log foldchange is computed, therefore
logarithmization might be necessary.
The p-values for the difference in means are based on a standard
normal assumption.
Martin Slawski martin.slawski@campus.lmu.de
Anne-Laure Boulesteix http://www.slcmsr.net/boulesteix
GetRepeatRanking, RankingTstat, RankingWelchT, RankingWilcoxon, RankingBaldiLong, RankingFoxDimmic, RankingLimma, RankingEbam, RankingWilcEbam, RankingSam, RankingBstat, RankingShrinkageT, RankingSoftthresholdT, RankingPermutation, RankingGap
## Load toy gene expression data data(toydata) ### class labels yy <- toydata[1,] ### gene expression xx <- toydata[-1,] ### run RankingFC FC <- RankingFC(xx, yy, type="unpaired")