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

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

Description

This function returns the betaHats for all genes in the corresponding GeneSet in the given experiment, or a list of such vectors for each set in a GeneSetCollection. This corresponds to each gene's contrubution to the test statistic. This method is applicable for all three approximation methods.

Usage

    betaHats(object)

Arguments

object

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

Methods

signature(object = "npGSEAResultNorm")

Returns the betaHats used for analysis to create a npGSEAResultNorm object

signature(object = "npGSEAResultBeta")

Returns the betaHats used for analysis to create a npGSEAResultBeta object

signature(object = "npGSEAResultChiSq")

Returns the betaHats used for analysis to create a npGSEAResultChiSq object

signature(object = "npGSEAResultNormCollection")

Returns the betaHats used for analysis to create the npGSEAResultNormCollection objects (1 for each set)

signature(object = "npGSEAResultBetaCollection")

Returns a list of the betaHats used for analysis to create the npGSEAResultBetaCollection objects (1 for each set)

signature(object = "npGSEAResultChiSqCollection")

Returns a list of the betaHats 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)
    betaHats(res) 

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