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

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

Description

This function returns the corresponding alpha value for the reference beta distribution for the npGSEA analysis in the gene set in the given experiment. This method is applicable for only the beta approximation method.

Usage

alphaValue(object)

Arguments

object

An object of type npGSEAResultBeta or npGSEAResultBetaCollection

Methods

signature(object = "npGSEAResultBeta")

Returns the value for alpha for a npGSEAResultBeta object

signature(object = "npGSEAResultBetaCollection")

Returns a list of the alpha values for a npGSEAResultBetaCollection objects (1 for each set)

Author(s)

Jessica L. Larson

See Also

npGSEAResultBeta-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, approx= "beta")  
    alphaValue(res)

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