computeChiSquaredTest: Compute chi-squared test

In wikum/divergence.preSE: Divergence Computations

Description

Given a binary or ternary data matrix with class associations of samples, computes chi-squared tests for each feature between given groups

Usage

computeChiSquaredTest(Mat, Groups, classes)

Arguments

Mat	Matrix of digitized binary or ternary data with each column corresponding to a sample and each row corresponding to a feature
Groups	Factor indicating class association of samples
classes	Vector of class labels; the test will be applied between the classes given.

Value

A data frame with columns 'statistic' and 'pval'.

Examples

baseMat = breastTCGA_Mat[, breastTCGA_Group == "NORMAL"]
dataMat = breastTCGA_Mat[, breastTCGA_Group != "NORMAL"]
div = computeUnivariateDigitization(
  Mat = dataMat,
  baseMat = baseMat,
	 parallel = TRUE
)
sel = which(colnames(breastTCGA_Mat) %in% colnames(dataMat))
div.chi = computeChiSquaredTest(Mat=div$Mat.div, 
                                Groups=breastTCGA_ER[sel],
                                classes=c("Positive", "Negative"))

wikum/divergence.preSE documentation built on Nov. 19, 2021, 3:37 a.m.