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

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

Description

This function returns the chi-sq statistic (which is compared to a reference Chi-sq distribution) for the chi-sq approximation of npGSEA for a corresponding GeneSet or a list of these statistics for a GeneSetCollection. This method is applicable for only the chi-sq approximation method.

Usage

chiSqStat(object)

Arguments

object

An object of type npGSEAResultChiSq or npGSEAResultChiSqCollection

Methods

signature(object = "npGSEAResultChiSq")

Returns the chi-sq statistic for a npGSEAResultChiSq object

signature(object = "npGSEAResultChiSqCollection")

Returns a list of the chi-sq statistics for a npGSEAResultChiSqCollection objects (1 for each set)

Author(s)

Jessica L. Larson

See Also

npGSEAResultChiSq-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= "chiSq")  
    chiSqStat(res)

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