xSet-methods {npGSEA} | R Documentation |
xSet
~~This function returns the scaled and centered expression data
for all genes in the corresponding GeneSet
in the given experiment,
or a list of such matrices for each set in a GeneSetCollection
.
This method is applicable for all three approximation methods.
xSet(object)
object |
An object of type |
signature(object = "npGSEAResultNorm")
Returns the centered and
scaled X matrix used for analysis to create a npGSEAResultNorm
object
signature(object = "npGSEAResultBeta")
Returns the centered and
scaled X matrix used for analysis to create a npGSEAResultBeta
object
signature(object = "npGSEAResultChiSq")
Returns the centered and
scaled X matrix used for analysis to create a npGSEAResultChiSq
object
signature(object = "npGSEAResultNormCollection")
Returns a list of
centered and scaled X matrices used for analysis to create the
npGSEAResultNormCollection
objects (1 for each set)
signature(object = "npGSEAResultBetaCollection")
Returns a list of
centered and scaled X matrices used for analysis to create the
npGSEAResultBetaCollection
objects (1 for each set)
signature(object = "npGSEAResultChiSqCollection")
Returns a list of
centered and scaled X matrices used for analysis to create the
npGSEAResultChiSqCollection
objects (1 for each set)
npGSEAResultNorm
-class
set.seed(15) yFactor <- as.factor( c(rep("treated", 5), rep("control", 5)) ) xData <- matrix(data=rnorm(length(letters)*10) ,nrow=length(letters), ncol=10) rownames(xData) <- letters geneSetABC15 <- GeneSet(geneIds=letters[1:15], setName="setABC15") res <- npGSEA(x = xData, y = yFactor, set = geneSetABC15) head( xSet(res) )