Description Usage Arguments Methods See Also Examples

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.

1 | ```
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

1 2 3 4 5 6 7 | ```
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) )
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.