xSet-methods: ~~ Methods for Function 'xSet' ~~

In npGSEA: Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)

Description

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.

Usage

    xSet(object)

Arguments

object

An object of type npGSEAResultNorm, npGSEAResultBeta, npGSEAResultChiSq,npGSEAResultNormCollection, npGSEAResultBetaCollection, or npGSEAResultChiSqCollection

Methods

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)

See Also

npGSEAResultNorm-class

Examples

    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) )

npGSEA documentation built on Nov. 8, 2020, 6:49 p.m.