updateContrastMatrixWithSV: Update a contrast matrix given a surrogate variable matrix

In bedapub/ribiosNGS: Utilities for next-generation sequencing data analysis in ribios

Update a contrast matrix given a surrogate variable matrix

Description

Update a contrast matrix given a surrogate variable matrix

Usage

updateContrastMatrixWithSV(contrastMatrix, svMatrix)

Arguments

contrastMatrix	A contrast matrix
svMatrix	A surrogate-variable matrix, for instance returned by sva

Value

An updated matrix, with surrogate matrix variables appended to the rows

Examples

exCounts <- matrix(rpois(12000, 10), nrow=2000, ncol=6)
exCounts[1:100, 2:3] <- exCounts[1:100,2:3]+20
exDesign <- model.matrix(~gl(2,3))
colnames(exDesign) <- c("Baseline", "Treatment")
exContrast <- limma::makeContrasts("Treatment"="Treatment", levels=exDesign)
exVoomSvaRes <- voomSVA(exCounts, exDesign)
updateContrastMatrixWithSV(exContrast, exVoomSvaRes) 

bedapub/ribiosNGS documentation built on Feb. 10, 2025, 12:34 a.m.